Future phosphorus (P) shortages could seriously affect terrestrial productivity and food security. We investigated the changes in topsoil available P (AP) and total P (TP) in China's forests, grasslands, paddy fields, and upland croplands during the 1980s–2010s based on substantial repeated soil P measurements (63,220 samples in the 1980s, 2000s, and 2010s) and machine learning techniques. Between the 1980s and 2010s, total soil AP stock increased with a small but significant rate of 0.13 kg P ha−1 year−1, but total soil TP stock declined substantially (4.5 kg P ha−1 year−1) in the four ecosystems. We quantified the P budgets of soil–plant systems by harmonizing P fluxes from various sources for this period. Matching trends of soil contents over the decades with P budgets and fluxes, we found that the P‐surplus in cultivated soils (especially in upland croplands) might be overestimated due to the great soil TP pool compared to fertilization and the substantial soil P losses through plant uptake and water erosion that offset the P additions. Our findings of P‐deficit in China raise the alarm on the sustainability of future biomass production (especially in forests), highlight the urgency of P recycling in croplands, and emphasize the critical role of country‐level basic data in guiding sound policies to tackle the global P crises.