Long-term stability is crucial in cropland for maintaining stable agricultural production and ensuring national food security. However, relatively few studies have been conducted on the long-term stability of cropland at the national level. This study assessed the long-term stability of cropland in China from 1990 to 2018 using a fine-resolution land use dataset. The experimental results indicated that the average area of unstable cropland in China from 1990 to 2018 amounted to 2.08 × 106 km2, 47.31% of the total. The Qinghai–Tibet Plateau exhibited the highest average proportion of unstable cropland at 65.9%, followed by the northern arid and semiarid region, Southern China, and the Yunnan–Guizhou Plateau. The quantity of unstable cropland in China initially declined before increasing, reaching a final growth rate of 5.09%. Furthermore, this study explored the relevant driving factors of cropland’s long-term stability from both natural factors and human activities based on artificial neural networks. The relative importance of distance to vegetation reached a value of 0.30, indicating that it had the most significant influence on the long-term stability of cropland, followed by relief amplitude and soil type. This phenomenon may be attributed to the inadequate execution of the Grain for Green Policy and the requisition–compensation balance of cropland policy, along with the depletion of young and middle-aged laborers due to urban migration from rural areas. Local governments should focus on addressing the unsustainable exploitation of sloped land in rural mountainous or hilly regions while preventing urban developers from appropriating fertile cropland to compensate for less fertile areas.