Non-uniform heating has been a challenging problem in microwave heating due to ‘standing wave pattern’ and ‘thermal runaway’ problems. Cycled microwave heating was used to improve microwave heating uniformity of frozen products, while a relatively new approach of inverter heating was claimed to help preserve food quality during thawing/heating. In this study, finite-element-method-based coupled multiphysics-kinetic models were developed, validated, and used to investigate these controversial results by comparing the heating performances of average temperature, heating non-uniformity, and nutritional value change between the inverter and cycled microwave heating of foods. The effect of food sizes/shapes and material properties (dielectric loss) was evaluated. Results showed that there was little difference in average temperature, heating uniformity, and Vitamin C content between cycled and inverter heating for different food products. A relatively more uniform heating and lower nutritional value degradation were observed for small size low loss material; however, the improvement was not significant enough to claim the benefit of inverter heating.