Municipal solid waste incinerator (MSWI) bottom ash is often used as the protection layer for the geomembrane and intermediate layer in the landfill. In this study, three sets of simulated landfills with different mass proportion of MSWI bottom ash layer to municipal solid waste (MSW) layer were operated. Cu and Zn concentrations in the leachates and MSW were monitored to investigate the effect of MSWI bottom ash layer on the Cu and Zn discharge from the landfill. The results showed that the Zn discharge was dependent on the mass proportion of MSWI bottom ash layer. The pH of landfill was not notably increased when the mass proportion of MSWI bottom ash layer to MSW layer was 1 : 9, resulting in the enhancement of the Zn discharge. However, Zn discharge was mitigated when the mass proportion was 2 : 8, as the pH of landfill was notably promoted. The discharge of Cu was not dependent on the mass proportion, due to the great affinity of Cu to organic matter. Moreover, Cu and Zn contents of the sub-MSW layer increased due to the MSWI bottom ash layer. Therefore, the MSWI bottom ash layer can increase the potential environmental threat of the landfill.