The main objective of this study is to analyze the historical change and current status of fish species diversity of the Chaobaihe River Basin. We statistically compile the species composition of the fish in the Chaobaihe River Basin before the construction of Miyun Reservoir based on the historical fish specimens and research literatures, and compares it with the survey data of 23 collection sites in the Chaobaihe River basin in 2017, collection sites as shown in Fig. 1. Depending on the analysis and comparison, there were at least 47 species of native fish species before the construction of Miyun Reservoir in this basin. And now it reduced to 33 species, as shown in the Table 1 and the appendix. In addition, there are at least 8 introduced species in the basin, as shown in the Table 1. Cyprinid fishes in the Chaobaihe River Basin accounts for 67% of the total number of species. Most of them are low trophic level fish species. Zacco platypus is the dominant species. The fish diversity and spatial changes of six rivers in the basin were evaluated by Margalef richness index, Shannon-Wiener diversity index and Pielou′s evenness index, the result of analytical computation as shown in Fig. 2, 3, 4 and 5. By analyzing the results we can see the degree of diversity of the mainstream is obviously higher than that of the tributaries in this basin, affected by the regulation of Miyun Reservoir (Regulate data of Miyun Reservoir as shown in Fig. 7) the upper reaches of the Miyun Reservoir are obviously higher than the lower reaches, and the Baihe River is the most diverse one which needs to be protected. Compared with the survey results of the Beijunhe River system and the Yongdinghe River system in the same period, the fish species richness, species diversity and species equability in the Chaobaihe River Basin are better than those of other two river systems, the data comparison as shown in Figure 8. Miyun Reservoir is the receiving waterbodies for the mid-route of the South-to-North Water Diversion Project. In this context, we should pay more attention to alien species in the Chaobaihe River Basin.