Hybrid metal halide perovskite is a promising material for efficient photovoltaic cells and potential thermoelectric energy conversion. This paper investigates phonon thermal transport in iodine-vacancy-defect methylammonium lead iodide (MAPbI3) perovskite using molecular dynamics simulations. The results show that the iodine vacancy defects suppress the thermal conductivity of defective MAPbI3. This effect is enhanced with increasing the defect concentration. The reduction of thermal conductivity of MAPbI3 with iodine vacancy defects compared with the pristine counterpart is mainly attributed to the enhanced phonon anharmonicity and shorter phonon relaxation time due to the phonon-defect scattering. Although iodine diffusion is observed in MAPbI3 with iodine vacancy defects, defect migration has a limited impact on mass-transfer induced convective phonon transport, while it is a source of phonon anharmonicity. This study may provide guidance for theoretical research and industrial application of as-synthesized metal halide perovskites with intrinsic defects.