Abstract: Exploring the habitat suitability of Coilia mystus, a migratory fish in the Pearl River estuary, can provide a scientific basis for the protection and utilization of fishery resources of C. mystus. Based on the date collected by the bottom-trawl in the Pearl River Estuary during winter in 2019 and summer in 2020, we constructed the habitat suitability index (HSI) model of C. mystus, taking the water depth, bottom salinity, bottom temperature, as well as bottom dissolved oxygen as indicator environment indicators. The analytic hierarchy process (AHP) was used to calculate the weight of the indicators. The arithmetic mean (AMM) and the geometric mean (GMM) were used to build a model. Then a suitability curve was developed and the HSI of C. mystus was calculated. Results show that the optimal bottom salinities for C. mystus in the Pearl River Estuary in winter and summer were 21.03‰−30.55‰ and 20.25‰−25.82‰, respectively; the mass concentrations of suitable dissolved oxygen were 6.79–7.28 and 3.85–4.01 mg·L⁻¹, respectively; the suitable water depths were 11.69–20.10 and 7.80–9.23 m, respectively; the suitable bottom temperatures were 19.84–19.95 and 28.36–29.44 ℃, respectively. The sites with HSI value greater than 0.5 accounted for 17.39% of the total survey sites. The study shows that the suitability of C. mystus was low, and its suitable habitats in the Pearl River Estuary are mainly located in the Sousa chinensis Nature Reserve in the Neilingding sea area.