The health impacts caused by chemical fertilizer utilization have challenged long-term sustainable development in many countries, particularly developing countries. Based on the emergy analysis method, we estimated the temporal and spatial variations of the health costs, through atmospheric, water, and soil pathways, of chemical fertilizer utilization in China during the period from 1990 to 2012. The results showed an obvious increasing trend of health costs from 1.8 billion Yuan in 1990 to 23.0 billion Yuan in 2012, while the ratio of health costs to agriculture output value declined slowly and became stable in recent years. Regional differences were remarkable and were significantly correlated to the levels of economic development (r = 0.843 and p < 0.001) and crop-sown area in the region (r = 0.588 and p < 0.001). Economically developed regions, especially the eastern coastal provinces, had much higher costs than the western regions. Meanwhile, fertilizer consumption shifted from the eastern to the northwest region, which was the same as the health costs. This study provides a reference to estimate the health costs of fertilizer utilization, and the results highlight the importance of sustainable development in China.