Abstract: The evaluation of ecological effect before and after the implementation of major ecological restoration projects is a prerequisite for testing the effectiveness of restoration measures and optimizing adjustments. The spatio-temporal distribution of resources is one of the important indicator in this evaluation. In order to grasp the spatio-temporal distribution characteristics of fish resources in the Jiang’an Chongqing section of the main stream of the Yangtze River upstream protection zone during the initial period of the “Ten Year Fishing Ban”, we applied hydroacoustic analysis by using the SIMRAD EK80 split beam scientific echo detector for underwater acoustic detection in the December 2020 and May 2021, supplemented by fish resource surveys. The results showed that the average fish density in the Jiang’an-Chongqing section was 25.31 ind./1000 m³ during the dry season and 41.23 ind./1000 m³ during the wet season. The fish distribution in December 2020 and May 2021 was mainly concentrated in the Chongqing-Jiangjin section. The average target intensity of fish in dry season and wet season was –55.81 and –52.79 dB respectively, with no significant difference. The estimated average body length of fish was 17.97 and 24.36 cm, respectively. In the vertical direction, the density of fish detected by underwater acoustics showed a certain difference in December 2020 and May 2021. In December 2020, it was shown as lower layer > middle layer > upper layer, while in May 2021, it was shown as upper layer > middle layer > lower layer. We found 62 fish species belonging to 12 families in the fish resource survey, in which the small fish species such as Pelteobagrus vachelli, Pelteobagrus nitidus, Culter mongolicus and Hemiculteri bleekeri accounted for 50.21%. The study preliminarily explored the spatial distribution of fish in the reserve at different times, providing scientific basis for the protection of fish resources in the upper reaches of the Yangtze River. Additionally, the findings serve a valuable reference for assessing the ecological effect of the “Ten Year Fishing Ban” in the Yangtze River.