Axial flux PM machines, featured by compact size and high performance, are suitable for powertrains of electric vehicles. This paper studies the design and control of a totally enclosed axial flux PM integrated-starter-generator system. Torque density and volume benefits from large number of pole pairs when designing PM machines. However, the increased pole pair number decreases the switching-frequency-to-electrical-period ratio, and large power drives are troubled with limited switching frequency. To improve this situation, a control strategy named overmodulation technique with variable sampling frequency is proposed to improve the system performance in the nonlinear region. The heat dissipation potential of the inverter is fully utilized and the DC bus voltage utilization ratio is enhanced with this control strategy. Simulation results are carried out in which the current waveform is also improved.