The introduction of non-native fish species is known to have adverse effects on aquatic ecosystems, but their effect on plateau lakes is not well studied. In this study, we examined the effect of the Japanese smelt (Hypomesus nipponensis) invasion on the fish assemblage in Lake Erhai, a subtropical plateau lake in southwestern China. Through cluster analysis and non-metric multidimensional scaling (NMDS), we found a significant fish assemblage shift: the population of sharpbelly (Hemiculter leucisculus) fell by 67% in catch per unit effort (CPUE) from 2.262 to 0.741; topmouth gudgeon (Pseudorasbora parva) fell by 52% from 0.61 to 0.29; and icefish (Neosalanx taihuensis) plummeted by 88% from 0.736 to 0.088. Meanwhile, the numbers for crucian carp (Carassius auratus) improved by almost 185% from 1.82 to 3.36. A Pearson correlation analysis showed that these four species significantly correlated with the invasion of the Japanese smelt: sharpbelly (−0.71), topmouth gudgeon (−0.71), icefish (−0.62), and crucian carp (0.81). This study documented the expansion of invasive fish and their effects on native species over time, thus providing a case study of invasive fish as well as a theoretical basis for further research into interspecies interactions.