The abundant and widely distributed resources of small pelagic fish in marine ecosystems constitute significant targets for commercial fisheries. The Japanese anchovy (Engraulis japonicus) is a prominent representative of small pelagic fish and is considered one of the most commercially valuable species in the northwestern Pacific region. This species is crucial in the Yellow Sea marine ecosystem, serving as a vital food source for various marine predators and contributing to the area's overall biological diversity. However, the sustainability of anchovy populations is increasingly threatened by factors such as overfishing and climate change, which have led to notable inter-annual fluctuations in the catch quantities. Consequently, focusing on effectively recruitment of anchovy populations is essential for maintaining ecological balance, particularly during their early growth stages, which are critical for survival and long-term population stability. This study investigated the marine environment of the Yellow Sea and the complex internal mechanisms that affect the early growth of anchovies. By analyzing samples collected from 2016 to 2018, we used otolith microstructural analysis, a method that allows for precise tracing of hatching dates and the evaluation of growth patterns over time. Furthermore, we employed mixed-effects models to explore the relationships between intrinsic factors, specifically age and maternal effects, and the early growth of anchovies. The distance measured from the otolith core to the annulus, representing complete absorption of the yolk sac, served as an indicator of growth status during the yolk sac stage, providing a quantifiable measure of the maternal effect on the early growth of anchovy larvae. To assess the influence of environmental factors on early growth, we applied a combination of gradient forest models and generalized additive models (GAM). The selected environmental factors included sea surface temperature (SST), mixed layer depth (MLD), northward sea water velocity (V), eastward sea water velocity (U), sea surface height (SSH), sea surface salinity (SSS), and chlorophyll-a concentration (CHL). This analysis identified the three most significant environmental factors influencing early growth. By classifying anchovy larvae into two distinct age groups (˂ 15 days and 15–40 days old), we used sliding windows to examine the lagged effects of environmental factors on different age stages. A relative time window was integrated into our analysis, and to mitigate the impact of random occurrences among candidate environmental factors, we conducted 500 randomization trials. The environmental factors that showed lagged effects were incorporated as fixed external effects into the best fixed internal effects model for further analysis, which aimed to predict their impact on early growth. Our study indicated a close relationship between larval growth and intrinsic factors. Specifically, the daily increment of anchovy otoliths was positively correlated with age, revealing a gradual flattening of growth trends as age increased. This supports the "bigger is better" hypothesis, suggesting that larger individuals tend to have lower mortality rates, enhanced predation capabilities, and improved predator evasion. Moreover, the results showed a linear positive correlation with maternal effects, underscoring the notable influence that mothers have during the initial growth phase of anchovies. The "maternal effect" hypothesis posits that, compared to first-time spawners under average conditions, repeat spawners and physiologically superior females produce larger eggs, which provide more nutrition and energy during the early growth stages, thereby promoting growth. Despite quantifying the influence of intrinsic factors on early growth, the underlying mechanisms behind these effects remain unclear and warrant further exploration. The study identified SST, MLD, and SSS as the three most critical environmental factors affecting early growth. However, their relative importance varied by month, indicating different regulatory mechanisms for anchovies hatching in the same area during different times of the year. This study found that the lag effect of environmental factors on otolith growth was approximately one week. Among the three environmental factors analyzed, SST was the only factor exhibiting a lag effect, which varied with the age of the anchovy. For larval fish younger than 15 days, SST had a one-day lag effect on growth; for those younger than 40 days, the lag effect extended to two days. The relatively short lag time of SST on early growth in this study may be attributed to a previous study where anchovies reached an age of 90 days, whereas the maximum age in this study was 40 days. The high sensitivity of early larval fish to environmental changes resulted in a slightly longer lag effect of SST on 40-day-old anchovies compared to those that are 15 days old. This indicates that as the age of the anchovy increases, its physiological state may prolong the response time to environmental changes. Further predictive analysis suggests that the early growth of anchovies increases with increasing sea surface temperatures. Additionally, within the same temperature range, otolith increment widths for anchovy larvae aged 5–40 days were greater than those for larvae younger than 15 days. However, as indicated by the Generalized Additive Model (GAM) analysis, the relationship between SST and growth often becomes complex due to the synergistic influence of various factors. Therefore, future research should adopt an energy balance perspective to comprehensively elucidate the growth mechanisms of anchovies. This study integrates several models in the investigation of early growth in anchovies, providing a scientific basis for early growth and laying a foundation for the conservation and scientific management of anchovy resources in the Yellow Sea from the perspective of internal and external factors affecting early life history stages.