This study investigates the effect of waterproofing can on the electromagnetic performance and thermal characteristic of the electric motor, which is a major part of an integrated motor propulsor for unmanned vehicles. To satisfy the design target, the electromagnetic performance of a designed motor with variable thickness and materials of waterproofing can was examined by two-dimensional finite element analysis (FEA) considering its eddy current loss. The thermal problem of the motor with waterproofing was solved by using an analytical lumped parameter thermal network method based on the motor losses which was obtained from FEA. A 39-kW electric motor and proper waterproofing can be manufactured and tested to verify the analytical expectation.