Rural settlements are undergoing a reconstruction process in the context of rapid urbanization, which has a significant impact on ecological land. However, rural settlements encroaching on ecological land (RSEEL) and its associated ecological effects have been widely ignored. This paper aims to accurately and quantitatively evaluate the ecological disturbance caused by RSEEL in China’s rapid urbanization areas. An ecological disturbance index combining changes in both the scale and fragmentation was applied in Nantong, Eastern China. Three types, including jump expansion, extension diffusion, and internal filling, were identified in RSEEL. The results show that the jump expansion type accounted for the largest proportion (58.39%) at the patch level, whereas the extension diffusion was the dominant type at the village level, and the internal filling type was the least common. RSEEL unexpectedly did not make ecological land more fragmented due to the preference for small independent patches in most encroachment cases; hence, the degree of ecological disturbance caused by RSEEL was low in most areas of Nantong. When the encroachment type of RSEEL was combined with the ecological disturbance degree, it was found that the ecological disturbance caused by the jump expansion type was higher than that of the other two types, and extension diffusion and low-level disturbance was the main pattern observed in villages. The findings will contribute to our understanding of the dynamic relationship between rural settlement and ecological land and provide valuable information for rural settlement reconstruction under ecological civilization.