Exploring the flow intensity of virtual cultivated land is the key to improving the ecological compensation and food security policy. This study aimed to analyze the dynamic evolution, spatial convergence, and its affecting factors of the virtual cultivated land flow intensity. The spatial convergence model was used in this study. The results showed that, during 2000–2018, the growth rate of the surplus state of virtual cultivated land at the national level is less than that of the deficit state of virtual cultivated land in China. Moreover, the number of deficit provinces of virtual cultivated land flow intensity is increasing. The absolute β-convergence characteristics of the virtual cultivated land flow intensity are significant at the national, northeast, central, and western regions. Additionally, the conditional β-convergence exists at the national and four regional levels. Meanwhile, cultivated land resource endowment, population scale, regional economic development level, and agricultural mechanization level play an important role in the convergence process of inter-regional virtual cultivated land flow intensity. However, the influence degree of different control variables on different regional virtual cultivated land flow intensity is not consistent. Therefore, policymakers should pay attention to cultivated land resources’ spatial transfer mechanism when making regional cultivated land ecological compensation policies to coordinate the interesting relationship between the deficit area and surplus area of virtual cultivated land. Therefore, it is necessary to take the virtual cultivated land flow intensity as the reference index and use the combination of market guidance and government control to stimulus the stakeholders to protect cultivated land by taking different measures.