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The dissolution of unstable minerals such as feldspar and carbonate is currently recognized as the primary cause of the dissolution pores in most clastic rock reservoirs globally. However, research has shown that quartz dissolution pores generally occupy a certain proportion in foreland basins typified by the Kuqa Depression. This paper studied the dissolution characteristics of quartz through the thin section analysis of the Cretaceous Bashijiqike Formation reservoir in the Kuqa Depression and molecular dynamics simulations, the findings profoundly clarify the influence of stress on quartz dissolution. It was found that the dissolution of quartz grains in the study area is quite common based on thin section observations. The molecular dynamics simulation experiments comprise two sets of experiments: umbrella sampling and molecular dynamics simulation of dissolution process. Through the umbrella sampling, it was found that under lateral compressive stress conditions, the free energy barrier for quartz dissolution is reduced. In molecular dynamics simulation experiments, there is a notable substance exchange process between quartz and the solution, ultimately forming a transition layer with a thickness of several angstroms, this layer exhibits greater thickness under lateral compressive stress conditions. In the simulated closed fluid mineral reaction system, the dissolution products of quartz enter the solution for a period of time, then ultimately reprecipitate on the surface of quartz. Through thin section analysis and molecular dynamics simulation research, the atomic level process of quartz dissolution under lateral compressive stress conditions has been elucidated, it may provide a new perspective on the formation mechanism of deep and ultra-deep high-quality clastic reservoirs.