In South China, due to climatic factors, highly weathered granite is distributed across a large area and easily disintegrates after encountering water, causing many geological disasters and other problems. To determine the disintegration mechanism of highly weathered granite in South China, disintegration tests were carried out on highly weathered granite in the Fuzhou area under different immersion durations, cycle times, and flow rates, with the help of a self-designed disintegration test device. Moreover, the disintegration mechanism of the highly weathered granite was revealed using nuclear magnetic resonance (NMR) technology. The results demonstrated an increase in the cumulative relative disintegration with prolonged immersion time and the number of dry-wet cycles. Beyond a certain flow rate, the cumulative relative disintegration amount stabilized. There was a strong correlation between the steady disintegration rate and immersion time (or dry-wet cycles). The disintegration process of the highly weathered granite was divided into three stages: rapid, moderate, and stable disintegration. Notably, disintegration primarily occurred around the large pores. This study revealed that the variation in the immersion time (or wet-dry-scouring cycles) was fundamentally linked to changes in the relative volume of the large pores in the rock samples. These findings provide valuable insights for predicting and mitigating surface disasters on highly weathered granite slopes.