An extreme precipitation event occurred from 31 July to 1 August 2016 in the Yili River valley during which multiple stations experienced off-the-charts precipitation values. Using the NCEP/NCAR 0.25° × 0.25° reanalysis data, the China Meteorological Administration (CMA) ground multi-source-merged hourly precipitation product, and hourly ground precipitation observation data, we performed numerical simulation and diagnostic analysis of the atmospheric instability and its trigger mechanism during heavy precipitation using the Weather Research and Forecasting (WRF) model. The results showed that the interaction of systems with different scales and the influence of complex terrains were important factors causing the extreme heavy rainfall in the arid and semi-arid areas. The results also revealed that the following: (1) During the first precipitation phase, the eastward lower cold front triggered the convective available potential energy in the lower convective unstable layer, which resulted in a short-term first heavy precipitation stage in the Yili River valley. After the unstable wet convective energy was released in the early stage of convective precipitation, the symmetrical instability of the lower atmosphere gradually increased, which maintained and strengthened the second heavy rainfall stage in the Yili River valley. (2) A lower convective instability layer was present during the first strong precipitation phase, which was a conditional symmetric instability mainly generated by the baroclinic component of moist potential vorticity (M_pv2 )during the initial precipitation period and the second strong precipitation period. Among them, the changes in M_pv2 at the lower layer during the early stages of precipitation were caused by the wet atmospheric baroclinicity and the vertical shear of the lower horizontal wind. The variability of the M_pv2 in the lower layer during the second heavy precipitation stage was mainly caused by the wet atmospheric baroclinicity. (3) During the first heavy precipitation phase, the lower frontal and topographical lifting led to the rapid development of vertical movement, which caused precipitation on the southern and northern slopes of the mountain in the Yili River valley. The mesoscale cyclone on the east side of the valley was stable and moved little due to the blocking effect of the terrain, which was a direct starting mechanism for the occurrence of the short-term rainfall in the eastern region. During the second stage of heavy precipitation, the convergence areas of the middle and lower wind fields were superimposed, and the high- and low-front areas were superimposed during the climbing process. The frontogenesis of the cold front caused vertical circulation in the northeast of the valley, from which the upward movement further developed and was a major cause of the second heavy rainfall stage.