A low-temperature tempering staged drying process was proposed in this study to minimize quality degradation and improve drying efficiency during waxy corn drying. Experiments of continuous drying, low-temperature tempering drying, and low-temperature tempering staged drying were conducted to investigate the drying characteristics and quality of waxy corn. The results showed that the low-temperature tempering drying process could shorten the effective drying time and increase the drying rate during the latter stage of the drying process. Under the same hot air temperature, increasing the tempering temperature from 30 °C to 40 °C reduced the effective drying time by 20 min. The Modified Henderson and Pabis model exhibited the best fit to the experimental drying data (R² ≥ 0.9864). The microstructural images of the waxy corn flour showed no significant changes among the experimental groups. The color difference (ΔE) of the continuous drying group was higher than that of the other experimental groups. Both the low-temperature tempering drying process and the low-temperature tempering staged drying process caused less damage to the waxy corn with a relatively lower crack ratio, thereby leading to a reduced electrical conductivity value. The starch content of the 80 °C–60 °C–40 °C group was higher than that of the other experimental groups. Based on comprehensive evaluation of the drying characteristics, the color parameters, and the quality of the dried waxy corn, the 80 °C–60 °C–40 °C group represents a favorable alternative.