The fishing-ban effects in Yangtze River are mainly indicated by the community recovery of aquatic organisms. To identify the effects, the aquatic organism community monitoring is critically needed. However, monitoring duration, monitoring tools and monitoring sites may severely impact its result. The current study aims to identify the impacts of monitoring duration, monitoring tools and monitoring sites on the results of fish communities monitoring and then provide suggestions for the technical details of monitoring fish community. Here, we used gillnets and cages to monitor the fish communities for 15 consecutive days in 10 sites in the middle reaches of Yangtze River form May to July, 2021. Then, we analyzed the catch per day, the recorded species per day and the fish community structure per day to research the impacts of monitoring duration, monitoring tools and monitoring sites on the monitoring results. The results showed that the catch of each day varied day by day and the average catch per day of accumulated 11 days monitoring results reached a relative stable status. The fish community structure result of each day varied day by day and the fish community structure showed by the accumulated 15 days monitoring results reached a relative stable status. Nearly 70% detectable fish species (estimated by species accumulation curve analysis) could be monitored by accumulated 15 days monitoring. The types and sizes of fishing tools obviously impacted the monitoring results of fish species and community structures. The fishing durations obviously impacted the monitoring results of catch per day. There were obviously spatial variations among the fish community structures in different reaches of Yangtze River. It suggested that in the middle reaches of Yangtze River, (1) the monitoring duration of 15 consecutive days was suitable for the fish stocks and community structure, (2) an adaptive tool assemblage is essential, (3) the fish community structure assessment of a definite reach should be based on the monitoring results of the definite reach, rather than a neighbor reach, (4) checking the sufficiency and efficiency of raw monitoring data was essential for assessing the fish stocks and community structures. Overall, the current study could provide scientific supports for the monitoring and evaluation of aquatic organism resources in key waters of the Yangtze River Basin after the fishing-ban.