Reservoir operation resulting from river damming has altered the flow regimes of the river sections of reservoirs, inducing profound impacts on the spatiotemporal distribution of the early resources of fish species that spawn drifting eggs (FSDE) in the river sections of reservoirs. During the period of low water-level operation stage of the reservoir, the river section with flowing-water habitats is an important spawning river section compared those other sections of the reservoir. Fully understanding the status of early resource of FSDE and their response to hydrological and thermal characteristics in a reservoir's middle and tail reaches is of great significance for the restoration and promotion the scale of early resource. This paper intended to reveal the inter-annual variation in the species composition of eggs and larvae collected, as well as the spawning scale and distribution of fish spawning grounds in the middle and tail reaches of the Three Gorges Reservoir (TGR), through the daily sampling for eggs and larvae being conducted at the Fuling section from May to July in 2017-2020. The random forest model was further performed to clarify the relationships between the variations in the daily spawning scales and the hydrological, thermal patterns and process conditions, aiming to identify the key hydrological and thermal factors affecting the variations of spawning scales of different species. The results showed that: 1) 21 species of eggs were collected, including 3 species of fish eggs that endemic to the upper reaches of the Yangtze River, and the amounts of eggs of 6 fish species, including Rhinogobio cylindricus, Chanodichthys mongolicus, and Hemiculter bleekeri, etc., were dominant, which accounted for 88.76% of total number of eggs collected. 2) The scale of fish eggs each year was 83.04×10⁸ ind., 14.29×10⁸ ind., 20.43×10⁸ ind., and 22.83×10⁸ ind., respectively. 3) There were 6 main spawning grounds distributed in the upstream of Fuling sampling site in the TGR, where is an important spawning place for endemic fish species (e.g. R. cylindricus, R. ventralis, and Leptobotia elongata) in the upper reaches of the Yangtze River. 4) The daily spawning scales were mainly affected by the amounts of transparency and flow discharge during spawning, as well as flow or water level rising rate and accumulated water temperature before spawning, and the key hydrological and thermal factors that affect the natural reproduction were different among different species. This research provides data support for the implementation of fish resource protection measures, especially ecological regulation measures, in the TGR.