To study spatial variability of soil heavy metals may help reveal effects of human activities on soil heavy metals accumulation and provide important basic data for soil utilization and its pollution risk assessment. Based on systematical analysis of heavy metals, arsenic (As), cadmium (Cd), copper (Cu), mercury (Hg), lead (Pb), zinc (Zn) in the environmental media, such as soil, irrigation water, fertilizer, and plants of a greenhouse vegetable production system typical of the suburbs of Nanjing, spatial variability and accumulation of heavy metals in the soil was explored causes of the accumulation analyzed, and effect of the accumulation on plant uptake of heavy metals in this system discussed. Results show that (1) accumulation of Cu, Hg, Pb, and Zn in the soil was significant compared with that in open fields, and the average contents of Cu, Hg, and Pb in the soil were higher than the criteria set in the Environmental Quality Evaluation Standard for Farmland in Greenhouse Vegetable Production; (2) Large amounts of agro-inputs significantly affected spatial variability of soil properties, and hence, the spatial variability of soil Cu, Hg, Pb, and Zn in a similar way, for these elements were closely correlated with soil properties; and (3) The changes in soil properties and the accumulation of heavy metals strongly affected leaf vegetable’s uptake of heavy metals, and the former played a more important role.