The aim of this study was to explore the distribution characteristics, sources, ecological risks and health indexes of heavy metals in greenhouse vegetable soils (GVS) of vicennial cultivation. Concentrations of chromium (Cr), nickel (Ni), copper (Cu), zinc (Zn), cadmium (Cd), and lead (Pb) were detected, and principle component analysis and cluster analysis were conducted. The potential ecological risk index and health index of the metals were also calculated to evaluate their multi-effects. Concentrations of Ni, Cu, Zn, Cd, and Pb reached peaks in GVS duration of 6-10 or 11-15 years, representing the high metal accumulation. Additionally, concentrations of Cr were significantly higher during the first decade than the second decade of GVS duration, which may be related to its bio-accumulation and leaching. Metals in soil depths of 20-40 cm showed a trend of intensive accumulation, especially in the second decade of duration. Cluster analysis revealed that Cr, Ni, and Zn were mostly from similar anthropogenic activities, and significantly high Cd in the studied area indicated the excessive human input. Furthermore, risk index demonstrated that GVS duration of 6-10 years was in moderate ecological risk and GVS duration of the second decade had a high health index.