In China, greenhouse agriculture, which provides abundant vegetable products for human consumption, has been rapidly developed in recent decades. Heavy metal accumulation in greenhouse soil and products obtained have received increasing attention. Therefore, the availability and accumulation of cadmium (Cd), copper (Cu), nickel (Ni), lead (Pb), and zinc (Zn) and their association with soil pH, soil organic matter (SOM), inorganic nitrogen (IN), total nitrogen (TN), available phosphorus (AP), and planting year (PY) in greenhouse soils were analyzed. The results showed that the mean concentrations of available Cd, Cu, Ni, Pb, and Zn were 17.25 μg/kg, 2.89, 0.18, 0.36, and 5.33 mg/kg, respectively, while their suggested levels in China are 0.6, 100, 100, 120, and 250 mg/kg. Cd, Cu, and Zn might be mainly originated from fertilizer application. A lower soil pH significantly increased the available Cu, Ni, and Zn concentrations and reduced Cd, Cu, Ni, and Zn accumulation. A higher AP significantly increased the proportions of available Cu, Ni, and Zn and elevated Cd, Cu, and Zn accumulation. There was a strong positive correlation between Cd, Pb, and Zn availability and TN, while IN was negatively related to the availability and accumulation of Cu and Zn. It was concluded that chemical fertilizer application increased the availability of Cu, Ni, Pb, and Zn and the accumulation of Cd, Cu, and Zn. Manure application clearly elevated the accumulation and availability of Cd and Zn in greenhouse soil.