To elucidate the effects of energy input modes on energy efficiency and berry quality in continuous microwave drying, four energy input modes with variational working ways of magnetrons were investigated by using numerical simulation and bench experiments in a continuous microwave dryer. Energy efficiency was divided into absorption and conversion efficiency to study the change rule of drying process, and the retention rate of anthocyanins of berry’s representative nutrition ingredient was studied considering both of the temperature and its uniformity. Results indicate that the energy input modes affect the absorption efficiency by changing the distribution uniformity of electric field of material layer, and the conversion efficiency by altering the matching degree between the energy allocation and drying characteristics of berry, which are both determined by the ways of working magnetrons of different energy input modes. The conversion efficiency has a greater influence on the final energy efficiency, so the energy input mode should be paid attention to the provision of microwave energy by selecting proper way of working magnetrons according to the drying characteristics. The effect of temperature uniformity on anthocyanin degradation is more obvious with average temperature increasing gradually, where better uniformity of electric field strength should be provided to guarantee the quality of dried berry by adjusting the energy input mode. The research results provide significant insights to optimize the energy input mode of taking into account both the energy efficiency and dried quality of material.