Recently, greenhouse cultivation production (GCP) has grown rapidly and counts a large proportion of vegetable production in China. In this study, the accumulation, health risk and threshold values of selected heavy metals were evaluated systematically. A total of 299 paired soil and vegetable samples were collected from three typical intensive GCP systems along the typical area of northwest of China. Mean concentrations of Cd, Hg, As, Pb, Cr, Cu and Zn in greenhouse soils were 0.21, 7.12, 0.07, 12.60, 24.30, 74.75, 26.72 and 82.22 mg kg^-1, respectively. Compared to rootstalk and fruit vegetables, leafy vegetables had relatively high concentrations and transfer factors of heavy metals. The accumulation of heavy metals in soils was affected by soil pH and soil organic matter. The calculated hazard quotients (HQ) of the heavy metals by vegetable consumption decreased in the order of leafy > rootstalk > fruit vegetables. The HI values were all below 1, which indicates that there is a low risk of greenhouse vegetable consumption. Soil threshold values (STVs) of heavy metals in GVP system were established according to the health risk assessment. The relatively lower transfer factors of rootstalk and fruit vegetables and higher STVs suggest that these types of vegetables are more suitable for cultivation in greenhouse soils. This study will provide an useful reference for controlling heavy metals and developing sustainable GCP.