The spawning grounds are important areas for the survival and reproduction of aquatic organisms and play an important role in the replenishment of fishery resources. The density of fish larvae in the Pearl River Estuary (PRE) was analyzed to establish Habitat Suitability Index (HSI) based on marine environmental factors. Survey data and satellite remote sensing data, including sea surface temperature, sea surface salinity and chlorophyll a concentration, from 2014 to 2017 during April–September were analyzed. Results showed that the accuracy of the HSI model based on the larval density and environmental factors was more than 60%, and the distribution trend of HSI was consistent with the distribution trend of larval density. The HSI models constructed based on Arithmetic Mean Model (AMM), Geometric Mean Model (GMM) and Minimum Model (MINM) methods can better predict the spatial–temporal distribution of larvae in the PRE. Among them, the accuracy of the HSI model constructed by the AMM and GMM methods was the highest in April (71%) and September (93%); the accuracy of the HSI model constructed by the MINM method was the highest in June (70%), July (84%) and August (64%). In general, the areas with high HSI values are mainly distributed in the offshore waters of the PRE. The spatial–temporal distribution of larvae in the PRE was influenced by monsoon, Pearl River runoff, Guangdong coastal currents and the invasion of high-salinity seawater from the outer sea.