Stocking and replenishing fish are crucial for the ecological restoration of aquatic biological resources. Since 2017, a long-term stocking program of Hypophthalmichthys molitrix and Aristichthys nobilis has been underway in the Xixi River basin of the Jiulong River. To understand the status of fishery resources following this long-term stocking program, field surveys were conducted every two months from October 2023 to October 2024. Traditional netting, resource assessment and environmental DNA (eDNA) analysis methods were used to conduct a comprehensive assessment of resource abundance, stocking contribution and ecological adaptability. The research revealed that the annual survival rates for H. molitrix and A. nobilis were 40.25% and 48.19%, respectively. The current numerical ratio of H. molitrix to A. nobilis stands at 1.97:1, indicating that the survival number of H. molitrix is better than that of A. nobilis. No mature gonads were observed in any sampled individuals, demonstrating that the current population is highly dependent on artificial replenishment. This study provides valuable data support for aquatic resource restoration and ecological management in the Jiulong River Basin.