Saline-alkaline water, a substantial proportion of global aquatic resources, with China alone encompassing approximately 46 million hectares, characterized by high pH, elevated alkalinity, and ionic imbalance. Its extreme environment imposes substantial physiological stress on most aquatic animals, severely limiting its potential for aquaculture. Developing saline-alkaline aquaculture has emerged as a vital strategy to expand fishery production, for the rising global demand of aquatic products. Recent studies have explored the culture potential of several species for saline-alkaline water, such as Leuciscus waleckii, Micropterus salmoides, Litopenaeus vannamei, Scylla paramamosain and Exopalaemon carinicauda. The ridgetail white shrimp E. carinicauda is a eurythermal and euryhaline shrimp distributed over a wide geographical area throughout tropical, subtropical, and temperate coastal waters. It can survive in a multitude of environmental extremes, has a broad salinity tolerance of 2–44 and can survive in freshwater after domestication. Therefore, it is an ideal species for saline-alkali water aquaculture, and it was also successfully cultured in saline-alkaline regions such as Dongying (salinity 5–8, alkalinity 1.4–8.0 mmol/L) and Cangzhou (salinity 10–20, alkalinity 3.5–13.0 mmol/L), yielding considerable economic benefits. However, large-scale breeding of seedlings specifically adapted to saline-alkaline water has not yet been achieved. Although the optimal salinity range for berried females is known to be 10–20, the specific effects of combined saline-alkaline stress, particularly the key stressors of low salinity and high carbonate alkalinity typical of coastal saline-alkaline waters, on the reproductive performance of E. carinicauda remain poorly understood. Salinity-alkalinity stress can critically impair crustacean reproduction by affecting ovarian development, spawning success, and embryonic and larval development. Previous research on aquatic animals has largely focused on adaptive mechanisms such as ion transport and antioxidant responses, leaving a substantial knowledge gap concerning reproductive traits under such stress. This study investigated the impacts of low salinity, high carbonate alkalinity, and their combined stress on the reproductive biology of E. carinicauda. Specific objectives were to: (1) assess effects on vitellogenesis, gonadosomatic index (GSI), hepatosomatic index (HSI), and fecundity; (2) evaluate larval tolerance to saline-alkaline stress; and (3) elucidate associated histological and ultrastructural changes in ovarian and hepatopancreatic tissues. The findings are expected to provide a theoretical foundation for breeding E. carinicauda in saline-alkaline waters and for selecting stress-tolerant broodstock. The female E. carinicauda (with undeveloped ovaries) were exposed for 35 days to four water conditions: a control group (natural seawater, salinity 25, alkalinity 3 mmol/L), a low-salinity group (LS, salinity 5, alkalinity 3 mmol/L), a high-alkalinity group (HA, salinity 25, alkalinity 10 mmol/L), and a combined saline-alkaline group (SA, salinity 5, alkalinity 10 mmol/L). Reproductive parameters, including ovarian developmental stage, GSI, HSI, number of eggs, and egg diameter, were measured. Hatching rate and the time from nauplius larva stage to post-larval stage were recorded for zoea larvae. Ovaries and hepatopancreas tissues were examined to assess developmental progress and structural integrity. Transmission electron microscopy was used to examine subcellular alterations in hepatopancreas cells, with a focus on organelles such as the endoplasmic reticulum, mitochondria, and lysosomes. Results showed that the ovarian development rate was significantly lower in all stress groups compared with the control group (P < 0.05). Among stress treatments, the HA group exhibited a significantly higher ovarian development rate than both the LS and SA groups (P < 0.05). The 10th day of the experiment, no significant differences in gonadosomatic index were observed among the control, HA, and LS groups. The control group showed the highest number of fertilized eggs (563.00 ± 58.97 eggs), which did not differ significantly from that of the HA group but was significantly higher than those of the LS and SA groups (P < 0.05). Fertilized egg length was greatest in the HA group (841.83 ± 32.89 μm), with no significant difference from the control group, but significantly larger than in the LS and SA groups (P < 0.05). Saline-alkaline stress significantly reduced the hatching rate of nauplii and prolonged incubation time. Hatching rates in the LS, HA, and SA groups were all significantly lower than that of the control group (P < 0.05), while incubation times were significantly longer than that of the control group (P < 0.05). Histological analysis revealed that ovarian development in the SA group lagged significantly behind that in the control, LS, and HA groups. All stress groups showed markedly reduced yolk content and enlarged intercellular spaces between oocytes. In the SA group, hepatopancreatic cells appeared deformed, with disordered arrangement of B-cells and R-cells. TEM examination of the LS group showed dilated endoplasmic reticulum, mild structural disorganization, and multiple autophagic lysosomes in hepatopancreatic cells. In the HA group, several cells contained multiple autophagic mitochondria. Cells in the SA group displayed loose and sparse cytoplasmic matrices, reduced mitochondrial numbers, and disrupted cristae. Carbonate alkalinity of 10 mmol/L slowed the ovarian development rate of E. carinicauda but did not affect its fecundity trait. In contrast, low salinity (salinity 5) and combined saline-alkaline stress reduced the content of vitellogenin and yolk material in the ovaries by interfering with vitellogenin synthesis in the hepatopancreas, significantly delaying ovarian development and decreasing fecundity trait. Low salinity, high alkalinity, and combined saline-alkaline stress all reduced the hatching rate of larvae and prolonged the incubation time. Follow-up studies will focus on the impacts of high alkalinity and combined saline-alkaline stress on yolk synthesis, aiming to enhance the hepatopancreas’s resistance to damage and address the insufficiency of yolk synthesis in the organism. This work lays a groundwork for future molecular studies to identify key genes involved in reproductive-stage stress tolerance.