China is facing severe rural development challenges such as the degradation of rural leading industries and weakening of food production functions. The improvement of the agricultural structure of the rural territorial system and the improvement of economic, social security, ecological and other functions are the foundation for national food security and regional sustainable development. It is an important step toward rural revitalization. This research constructed evaluation system to assess the vulnerability of rural territorial system from three dimensions (i.e., exposure, sensitivity and adaptability) in Jilin Province between 2005 and 2019. The dominant factor method was used to analyze key factors of rural vulnerability in different counties. Entropy, factor analysis and comprehensive vulnerability evaluation model, were integrated to measure the vulnerability of rural territorial systems. While the sensitivity of the rural territorial system of Jilin Province had increased with significant fluctuations, the exposure and adaptability had decreased. The vulnerability of the rural territorial system of Jilin Province has a significant spatial variation, being low in the middle and west and high on both east and west portion of the province. The extremely and severely vulnerable counties are mainly in the west and the southeast, the moderately vulnerable counties are concentrated in the western and the northeastern. The mildly and slightly vulnerable counties are mainly concentrated in the central region. According to the dominant factors of the vulnerability of the rural territorial system, the study area were classified into 7 causal types. The dominant factors of the 14 counties with extreme and severe vulnerability are the sensitivity-adaptability and exposure-sensitivity-adaptability. For the 23 counties with moderate vulnerability, the adaptability is the dominant factor. For another 23 counties with mild and slight vulnerability, the adaptability and exposure-sensitivity-adaptability are the dominant factor. Accordingly, specific control measures include enhanced implementation of soil and water conservation, strengthening the prevention of geological disasters, increasing the fertility of medium and low-yield cropland, and strengthening government support and guidance, in order to improve the resilience of rural territorial systems in the Province.