China's rapid development of industrialization and urbanization causes the growing problem of heavy metal pollution of soil, threatening environment and human health. Therefore, prevention and management of heavy metal pollution become particularly important. Critical loads of heavy metals are an important management tool that can be utilized to prevent the occurrence of heavy metal pollution. Our study was based on three cases: status balance, water environmental effects and health risks. We used the steady-state mass balance equation to calculate the critical loads of Cd, Cu, Pb, Zn at different effect levels and analyze the values and spatial variation of critical loads. In addition, we used the annual input fluxes of heavy metals of the agro-ecosystem in the Yangtze River delta and China to estimate the proportion of area with exceedance of critical loads. The results demonstrated that the critical load value of Cd was the minimum, and the values of Cu and Zn were lager. There were spatial differences among the critical loads of four elements in the study area, lower critical loads areas mainly occurred in woodland and high value areas distributed in the east and southwest of the study area, while median values and the medium high areas mainly occurred in farmland. Comparing the input fluxes of heavy metals, we found that Pb and Zn in more than 90% of the area exceeded the critical loads under different environmental effects in the study area. The critical load exceedance of Cd mainly occurred under the status balance and the water environmental effect, while Cu under the status balance and water environmental effect with a higher proportion of exceeded areas. Critical loads of heavy metals at different effect levels in this study could serve as a reference from effective control of the emissions of heavy metals and to prevent the occurrence of heavy metal pollution.