Soil pollution is generally attributed as the main source of Pb in crops. However, there are relatively few studies on the effects of atmospheric deposition and soil stress on crops. In this study, we investigated the influence of Pb due to atmospheric deposition and soil stress on the growth, accumulation, chemical morphology, and physiological and biochemical responses of Amaranthus tricolor L. seedlings using Pb solution spraying and Pb contaminated soil pot experiments. The results indicated that both atmospheric and soil Pb stress can significantly increase the Pb content in the Amaranthus tricolor L. seedlings. Among them, the effect of soil concentration accounted for 62.64%, and the effect of atmospheric deposition accounted for 32.89%. Insoluble phosphate, pectin, and protein-bound state are the primary chemical forms of Pb. The atmospheric Pb stress alone promoted the growth of the Amaranthus tricolor L. seedlings and synthesis of soluble proteins; however, soil Pb stress exhibited an inhibitory effect, increased hydrogen peroxide and malondialdehyde content, and caused damage to the cell membrane system. Antioxidant enzymes (superoxide dismutase, peroxidase, catalase) and antioxidants (ascorbic acid, glutathione) exhibited positive and effective responses to the soil and atmospheric Pb stress. The research results provided an important scientific basis for the environmental risk assessment and pollution prevention of crops in areas under heavy stress from the atmosphere and soil.