Fishes are the important parts of aquatic ecosystems in the rivers. Fish migration or movement between mainstream and tributaries is not only common, but also usually closely associated with fish spawning activity. As an important component of the Jinsha River network, the lower reaches of the Jinsha River exhibit relatively abundance meta-habitats and higher fish species diversity. Studying the effect of fish spawning migration between the mainstream of the Jinsha River and its tributaries on the variations of fish assemblages in the tributaries, as well as the importance of tributary habitat maintenance for the preserve of local fish population size, are of great significances to protect the fish resources of the tributaries of the Jinsha River. Heishui River is one of the important tributaries in the lower reaches of the Jinsha River. In this study, we selected some river segments of Heishui River as a typical study region. Based on the monthly fish catch investigations in this study region in 2014, a variety of multivariate analysis methods including cluster analysis, distance-based linear model, distance-based redundancy analysis and other statistic methods were used for:determining whether the monthly changes in fish assemblage structures of the lower reaches of the Heishui River were heavily dependent on fish spawning migration between the mainstream of the Jinsha River and the lower reaches of the Heishui River, and determining whether the natural habitat of the lower reaches in the Heishui River was important for the maintenance of the local fish populations. The results showed that the fish assemblage structures of the lower reaches of the Heishui River were significantly separated in the rainy and dry seasons of the Jinsha River. This separation resulted from the significantly differences in abundances of eight indicator species between the rainy and dry seasons in the Jinsha River. Correspondingly, the abundances of sexual mature individuals of these eight species also showed some changes between the rainy and dry seasons. The variations in abundances of sexual mature individuals of seven indicator species could explain 77.20% of the total variations of fish assemblage structures of the lower reaches of the Jinsha River, herein the variations in abundances of sexual mature individuals of Schizothorax prenanti, Lepturichthys fimbriata and Paramisgurnus dabryanus were the three most significant factors affecting the variations of fish assemblage structures of the lower reaches of the Heishui River. Overall, the spawning migrations of seven indicator species have the significant impacts on the variations of fish assemblage structures of the lower reaches of the Heishui River. This study showed that under the background of serious hydropower developments in the mainstem and tributaries of the Jinsha River, keeping the existing natural habitat areas of the lower reaches of the Heishui River is very important for maintaining fish population survival of the lower reaches of the Jinsha River. For the implementation of the above objective, after the normal operation of the Baihetan reservoir, the removals of some small dams as well as other river re-naturalizing measures should be applied for maintaining the existing natural habitat area of the Heishui River.