The intense management practices in greenhouse production may lead to heavy metal (HM) accumulations in soils. To determine the accumulation characteristics of HM and to evaluate possible HM sources in greenhouse soils, thirty typical greenhouse soil samples were collected in Shouguang District, Shandong Province, China. The results indicate that the Cd, Cu, and Zn concentrations are, respectively, 164.8%, 78.6%, and 123.9% higher than their background values. In the study area, Cd exhibits certain characteristics, such as wide variations in the proportion of its exchangeable form and the highest mobility factor and geo-accumulation index, which are indicative of its high bioavailability and environmental risk. In addition, there is a significant positive correlation between pairs of Cd, P, soil organic carbon, and cultivation age. Combined with principal component analysis, the results indicate the clear effects that agricultural activities have on Cd, Cu, and Zn accumulation. However, Cr, Ni, and Pb have a significant correlation with soil Fe and Al (hydr)-oxides, which indicates that these metals mainly originate from parent materials. This research indicated that long-term intensive fertilization (especially the application of chemical fertilizers and livestock manure) leads to Cd, Cu, and Zn accumulation in greenhouse soils in Shouguang. And the time required to reach the maximum permeable limit in agricultural soils for Cd, Cu, and Zn is 23, 51, and 42 years, respectively, based on their current increasing rates.