Ecosystem integrity is the foundation of ecosystem health and is popular to quantitatively analyze ecosystem integrity using the Index of Biotic Integrity (IBI). The IBI was initially used as a water pollution index and has been widely applied in ecosystem health assessment, particularly in fish, benthos, and plankton. Phytoplankton is the primary producer in aquatic ecosystems and is sensitive to changes in environmental factors. The Phytoplanktonic IBI (P-IBI) has been increasingly used in the ecosystem health assessment of bays, rivers, lakes, and reservoirs. However, no reports are available on applying P-IBI in the estuary ecosystem. Based on P-IBI, this study constructed an ecological health assessment indicator system and built an evaluation criterion in the coastal waters of the Yellow River estuary. To evaluate the ecological health status, three surveys were conducted on phytoplankton in May, July, and December of 2020. A total of 31 sampling sites were set up in the study area (119°00′E–119°25′E, 37°20′N–38°05′N), and 73 species of phytoplankton from four phyla were collected, with diatoms being the major groups and the species number accounting for 82.19%. The reference points and damaged points were determined according to the Shannon-Wiener diversity index H´, and the sites with H´≥3 were reference points; the others were damaged points. Considering factors such as ecological characteristics of the study area, phytoplankton population distribution, and data availability, 13 biological indicators were selected as candidate indicators. Then, the core indicators of P-IBI in various months were identified by screening candidate indicators. First, the discriminant ability analysis was used to preliminarily select the indicators, and their IQ≥2 were retained. Second, Pearson correlation analysis was conducted for these indicators. The P-IBI core indicator system in May, July, and December contained four, five, and four biological indicators, respectively. The scores of each indicator were calculated using the ratio method. The 95% or 5% quantile of the core indicators in all sampling sites was regarded as the best expected value; for indicators which increased with increasing interference, the best expected value was 5% quantile. Conversely, for indicators which decreased with increasing interference, the best expected value was 95% quantile. Each indicator score was calculated using a different formula according to their response to interference. Accumulating all core indicator scores at the same site, the total P-IBI score for this site was obtained. The 25% quantile of the reference points P-IBI was taken as IBI-expected, the P-IBI range less than IBI-expected was quartered. The delineation standard for the ecological status grade was ascertained, and the ecological status level of each site was identified according to its total P-IBI. The ecological status of each site was marked by using 1, 3, and 5 approximations of value assignment, the marked scores of each site were summed up using the equal weight method, and standardization was conducted to eliminate the differences caused by various indicator numbers. The comprehensive evaluation index (CEI) of the coastal waters in the Yellow River estuary was achieved. The results showed that the ecological status in each site was different and the spatial distribution was significantly diverse for the three months. In May, a few sites were present with excellent levels (9.68%), and they were scattered around the mouth of the Yellow River. In July, the proportion of sites with excellent levels reached 35.48%, and they were mainly located in the estuary of the Yellow River and Laizhou Bay. In December, the proportion of sites with excellent status was approximately 38.71%, and they were concentrated in the waters north of the Yellow River estuary. In general, concerning the stations above “good” ecological level, 21 were present in May; 29, in July; and 26, in December; therefore, the ecological condition was slightly worse in May. P-IBI had a significant positive correlation with ammonium (NH4-N), a significant negative correlation with nitrate (NO3-N), phosphate (PO4-P), and dissolved oxygen (DO), and a significant positive correlation with sea surface temperature (SST). However, no significant correlation was observed between P-IBI and sea surface salinity (SSS), pH value (pH), nitrite (NO2-N), and silicate (SiO3-Si). The CEI indicated the health status was “fair” in the coastal waters of the Yellow River estuary in 2020. Selecting reference points and screening biological parameters were the key steps in constructing the P-IBI indicator system, which determined the science of the evaluation result and the practicality of regional health management. The detailed method was offered in this study, and it could provide information for other research projects. This study provided a reference for the health management and ecological restoration of this water area and offered data support for the ecological protection and high-quality development of the Yellow River Basin.