A survey of early fish resources in the Fujin section of the lower Songhua River was carried out to know about the status of early fish resources and the location of spawning grounds from June to July in 2016—2018. A total of 8916 eggs and 31232 larvae were collected. A total of 33 species belonging to 7 families and 3 orders were identified by morphological and molecular biological methods. Among them, 12 fish species produced drifting eggs and floating eggs. The estimated abundance of fish eggs flowed through the Fujin section was 85.58×10⁸ eggs, 57.43×10⁸ eggs and 60.51×10⁸ eggs from 2016 to 2018, respectively. The dominant species were Hemiculter bleekeri bleekeri, Gobiobotia pappenheim and Saurogobio dabryi, and the abundance of fish eggs was 143.35×10⁸ eggs, 15.62×10⁸ eggs and 7.19×10⁸ eggs during the surveys, respectively. The spawning amount of these three dominant fishes accounted for 64.56% of the total spawning amount. The abundance of fish eggs of drifting egg fishes Hypophthalmichthys molitrix and Culter alburnus, and floating egg fishes Elopichthys bambusa and Siniperca chuatsi was 1.36×10⁸ eggs, 3.19×10⁸ eggs, 2.77×10⁸ eggs and 0.32×10⁸ eggs, respectively. According to the analysis of the developmental period and flow rate, the spawning grounds of Hypophthalmichthys molitrix originated from the Dulu River estuary to the Dailiangzi River in Huachuan County and from Suwopeng to the Zhonghe Village section. Redundancy analysis results showed that the drifting density of Hemiculter bleekeri bleekeri eggs was significantly correlated with transparency and that of Hypophthalmichthys molitrix, Culter alburnus, and Elopichthys bambusa was significantly correlated with water temperature and flow. In order to more effectively protect the fish resources of the lower Songhua River, it was recommended to increase the releasing number of fishes such as Ctenopharpharyngodon idellus, Mylopharyngodon piceus (Richardscn), Megalobrama skolkoui (Dybowski) and Culter mongolicus mongolicus (Basilewsky); establish a comprehensive prevention and control system for soil erosion in the Songhua River Basin to reduce the impact of soil erosion and water pollution on fish habitats; develop aquatic biodiversity observation, early warning, and evaluation systems to monitor key areas and key populations. Based on the scientific research and judgment of the monitoring results, we should adjust and optimize the Songhua River aquatic life protection measures.