Mortality is one of the crucial factors influencing fish population dynamics. The fish instantaneous mortality rate is a key parameter depicting the process and characteristics of fish death, and it holds significant theoretical and practical importance in fishery stock assessment and management models. However, it was often neglected due to assessment difficulties. To understand the mortality characteristics of plateau Schizothoraciae fish in China and explore suitable methods for assessing their instantaneous mortality rate, this study analyzed the population of Gymnodiptychus pachycheilus (189 individuals) collected from the middle reaches of the Yalong River from 2020 to 2021. The total instantaneous mortality rate (Z) was estimated using the weighted linear regression, Chapman-Robson method, and the Beverton-Holt method. The Natural Mortality Tool (NMT) was used to estimate the instantaneous natural mortality rate (M) and assess the reliability of all these estimates. Additionally, the Maunder model was employed to analyze the impact of sex and age differences on the M of G. pachycheilus. Meanwhile, the NMT was used to estimate M of 26 stock of 18 Schizothoraciae species (including G. pachycheilus). The results indicated that the Z estimated by the Chapman-Robson and weighted linear regression methods (0.88 year-1 and 0.89 year-1, respectively) were more reliable than that estimated by the Beverton-Holt method. Methods based on maximum capture age and growth parameters tend to overestimate and underestimate M of G. pachycheilus respectively. However, the M estimated by the weighted combination using NMT (0.23 year-1) proved more reliable than using traditional single-method, with the corresponding fishing instantaneous mortality rate (F) between 0.65 and 0.66 year-1. This suggests that the G. pachycheilus population in the middle reaches of the Yalong River may be facing significant environmental pressures (including fishing death caused by illegal fishing, and natural death caused by pollution and habitat loss). Furthermore, the Maunder model analysis revealed that G. pachycheilus faces a minor peak of natural death upon entering the reproductive phase, other than the high mortality levels of the juvenile stage. The M of females was higher than that of males only between the ages of 4.71 and 5.31, while it was lower for females at other times. Most Schizothoraciae fish in other studies exhibited a similar pattern where the M of females exceeded that of males. Additionally, the study found that Schizothoraciae fish classified as highly specialized and specialized species (including G. pachycheilus) generally had a higher M compared with those classified as primitive species, and the latter had lower and more dispersed M. Based on these results, it is feasible to develop a general method evaluate the M for Schizothoraciae fish in China, and the M could be a valuable indicator to assess the population dynamics