Early warning of soil environmental quality is an important basis for implementing classified and graded soil risk management measures. To quickly understand the regional soil environmental quality and take effective measures in time to prevent continuous soil pollution before deterioration of soil environmental quality, a simple, effective, and quantifiable early warning system for soil environmental quality of agricultural land and development land was respectively established based on environmental capacity and pollutant input-output flux theory. Furthermore, corresponding method and mechanism for early warning were defined based on soil environmental quality standards, food safety standards, and carcinogenic risk coefficients. The agricultural land in Youxian county and the development area within the fifth-ring in Beijing were chosen to assess the soil environmental quality and predict risks of heavy metals exceeding standards in different scenarios. The results show that the soil environmental quality of the agricultural land in Wangling and Taoshui Town both can be classified to the fifth early warning level. Compared with other remediation measures, the Cd contents of soil can be lowered to risk screening levels in the short term by the scenario of "paddy straw not returned to the field". The soil quality in the development area within the fifth-ring in Beijing belongs to the first early warning level under both the "no intervention" and the "decreased input" scenarios, which means that Cd, Cu, Pb, and Zn all need more than 50 years to reach their threshold values to pose potential health risks.