Natural convection and heat transfer in a square cavity with multiple heat sources was investigated through a multiple-relaxation-time (MRT) collision model and lattice Boltzmann method (LBM) in the current work. The MRT-LBM model was verified by a former experiment and numerical findings with different Ra numbers from 103 to 105, which proved the MRT-LBM model is effective to handle the flow and transfer. The heat transfer that developed inside the cavity was analyzed under different width, height, and lateral offset of heat source in this paper. Moreover, the change of spacing between two symmetrically distributed heat sources was discussed. The results showed that the heat exchange efficiency was augmented by increasing width, height, and spacing of the heater, but it was reduced by increasing lateral offset. Specifically, the Nusselt number of the upper wall decreased by increasing height of heat source, and the left and right walls showed better heat exchange efficiency by increasing height. Additionally, the lateral position had a notable influence on the left wall surface of the heat source, and the optimum heat exchange efficiency of the heat source’s left wall existed in the condition of small lateral offset.