The Heilongjiang River is located in a high-latitude cold region, and the natural Reproduction and early-stage resource occurrence of fish have their own uniqueness. Understanding the spatial patterns of drifting fish eggs species and community structure is of great significance for the conservation of Heilongjiang River fish resources. From June to July 2022, a monitoring study of drifting fish eggs was conducted in three river sections of the Heilongjiang River main streams: Fuyuan, Qindeli, and Luobei. DNA barcoding technology was used to identify the species of fish eggs, resulting in the acquisition of 1179 CO I gene sequences, identifying a total of 15 fish species belonging to 2 orders, 3 families, 8 subfamilies, and 15 genera. Among them, the Cyprinidae family was the most represented with 13 species, accounting for 83.29%, followed by one species each in the Cobitidae and Sinipercidae families, accounting for 16.45% and 0.25% respectively. The analysis results showed that the species composition of drifting fish eggs was mainly composed of small fish such as Hemiculter bleekeri, Parabotia fasciatus, and Gobiobotia pappenheimi. Community diversity was highest in the Fuyuan section and showed a decreasing trend upstream, demonstrating clear spatial heterogeneity. The relative importance index (IRI) of important economic fish species such as Hypophthalmichthys molitrix, Ctenopharyngodon idella, Elopichthys bambusa, Culter alburnus, Parabramis pekinensis, and Siniperca chuatsi shows a significant decreasing trend from Fuyuan (downstream) to Luobei (upstream), implying that the spawning stock in the Fuyuan section is larger than in the upstream sections, while the resources in the Luobei section are facing decline. This study suggests that environmental factors and overfishing are likely the main factors affecting the early resources of important economic fish species. It is recommended to establish fishing bans and closed seasons in spawning grounds, reduce fishing intensity, and conduct long-term monitoring studies of early resources such as fish eggs and larvae to scientifically protect and rationally utilize Heilongjiang River fishery resources.