To investigate the effects and relative contributions of soil and atmospheric deposition on cadmium (Cd) and lead (Pb) accumulation in leafy vegetables, this study collected soils with low, medium, and high Cd and Pb concentrations from Nanjing (Jiangsu), Kunshan (Jiangsu), and Lanping (Yunnan), respectively. Pot and field experiments were simultaneously conducted under two planting conditions (inside a greenhouse to exclude atmospheric deposition and outside under open-air conditions) at a typical vegetable production base along the Yangtze River in Nanjing. The results showed that soil Cd concentration was the dominant factor controlling Cd accumulation in pakchoi. In the high?Cd soil, even when grown inside the greenhouse, the Cd concentration in pakchoi (0.23 mg/kg) exceeded the food safety limit (0.20 mg/kg). The contribution rate of atmospheric deposition to Cd accumulation was highest (29.7%) in the low?Cd soil, and was 15.7% and 28.1% in the medium? and high?Cd soils, respectively. This indicates that atmospheric deposition is the main source of Cd accumulation in pakchoi when soil Cd concentrations are low, whereas soil becomes the dominant source when soil Cd concentrations are high. For Pb, the contribution of atmospheric deposition was generally low and not statistically significant; however, extending the planting period to 45 days increased Pb concentrations by 2–6 times, suggesting that the risk of long?term Pb exposure should not be ignored. The field experiment further confirmed that prolonged planting period promotes Pb accumulation in pakchoi under natural conditions, as Pb concentrations increased significantly with extended growth period. This study provides a scientific basis and data support for the source prevention and control of heavy metal pollution in farmland soils and for the safe production of agricultural products.