Amidst the ongoing rapid urbanization and escalating population mobility, gaining a profound understanding of population shifts in county rural areas is paramount for fostering integrated urban-rural development. Leveraging precise geographic data on rural settlements, including settlement patches and LandScan - a high-resolution population distribution dataset - we innovatively devised a population contraction index. This index systematically tracks the dynamic changes in population density at the patch scale across China's rural settlements from 2000 to 2020. Our comprehensive analysis encompasses population contraction within 2,847 counties nationwide, revealing distinct spatial distribution patterns. The findings indicate: (1) Notable concentrations of shrinkage patches in the Huaihe River Basin, with western settlements primarily experiencing mild shrinkage and eastern coastal settlements mostly undergoing heavy shrinkage. (2) At the county level, rural population contraction exhibits significant regional disparities, characterized by a spatial configuration of "two belts and multiple agglomerations." Administrative divisions further differentiate population contraction traits among counties and cities. (3) Urbanization (UR), educational services (EDU), and agricultural mechanization (ARG) are the pivotal factors shaping rural county contraction in China. Notably, the interplay between educational service level and rural income level wields the strongest explanatory influence. This research aims to furnish a robust empirical foundation and scientific direction for dissecting the human-land nexus within counties, refining rural settlement planning, and advocating for efficient, intensive resource utilization.