A motor controller for a motor-driven compressor includes a compressing body for compressing and discharging a refrigerant and a motor including a rotary shaft, the motor for driving the compressing body through the rotary shaft. A coil of the motor is arranged in a refrigerant containing area in the motor-driven compressor. The motor controller includes a determining section for determining whether liquid refrigerant is present in the refrigerant containing area and a modulation control section for driving the motor in accordance with three phase modulation control or two phase modulation control based on a determination result of the determining section.