Owing to several human economic activities (such as application of municipal sewage sludge, atmospheric deposition of Cd, mining activities, application of chemical fertilizers and pesticides), lead (Pb) and cadmium (Cd) contamination of soils has become more and more serious in China. The effects of different intercropping systems, namely, monoculture of corn (Zea mays var. Tiandan No. 8), corn/lupin (Lupinus luteus L.) and corn/chickpea (Cicer arietinum L.) on uptake and accumulation of Pb and Cd by these plants in soils contaminated with heavy metals were investigated in a greenhouse experiment. For intercropping treatments, there were the following separation modes: (1) no separation; (2) separation by a plastic barrier to eliminate root contact and solute movement; and (3) separation by a nylon mesh (30 μm) to prevent root contact but to allow solute exchange. The results showed that there were significant changes in biomass (shoot and root) of different crops under different intercropping and separation modes. The concentrations of Pb in the roots of corn were significantly affected by different intercropping systems and different separation modes, but Pb in the shoot of corn were not significantly different between separation modes. Pb concentrations were lower in the roots of corn cultivated in the compartments separated by plastic barrier or in corn/chickpea intercropping systems. The concentrations of Cd in the shoot of corn were not significantly affected by both separateion modes and different intercropping systems, but there was significant difference in Cd accumulation in the roots of corn between separation modes. The changes in concentrations of Pb and Cd in lupin and chickpea plants under different intercropping systems and different separation modes were also discussed. The concentrations of Pb in rhizosphere soil solutions decreased with growth time, but the reverse was true for Cd. Pb and Cd concentrations in rhizosphere soil solutions were also affected by intercropping systems or separation modes.