Global agriculture is facing an aging workforce and successor crisis, while the degradation of rural youths’ agricultural skills, which is indeed a concrete manifestation of young agricultural labor loss, has received little attention. Based on data from 1902 questionnaires in rural Southwest China, this study draws on a qualitative and quantitative analysis of the degradation of their skills to deepen the insights into the relationship between rural youth and agriculture. We found that rural youth have much lower agricultural skills than rural middle-aged and elderly residents, and their agricultural skills vary depending on gender, age, and occupation. Rural young non-agricultural workers’ large proportion among rural youth and low skills are the main sources of the reduction in rural youths’ skills. According to ordered logistic regression analysis, rural young non-agricultural workers who are older, have less education per person in their household, and have a larger cultivated land size have higher skills. As for rural students, 65.44% of the rural students have no skills, age and family’s agricultural income are significant positive influencing factors of their agricultural skills, and female youth have higher agricultural skills. The results provide references for policymakers to formulate targeted policies to cultivate rural young agricultural successors.