Sea buckthorn has garnered significant attention owing to its nutritional richness; however, it has a limited shelf life. In this study, the drying process of sea buckthorn was categorized into the first-, second-, and third-drying stages. Regression models were employed to examine the effects of the drying temperature, relative humidity of the medium, and prolonged high humidity retention on various parameters during the first- and second-drying stages. Comparative analysis revealed that the optimal drying conditions for the first-drying stage of sea buckthorn were a drying temperature of 80 °C, relative humidity of 28%, and high humidity retention time of 84 min. In the second-drying phase, the optimal conditions were a drying temperature of 78 °C, a relative humidity of 17%, and a high humidity retention time of 84 min. One-way optimization revealed that the optimal drying temperature for the third-drying stage was 70 °C. The implementation of temperature- and humidity-controlled infrared hot-air drying (TH-IRHAD) techniques considerably improved the outcomes. Specifically, the drying time, energy consumption, and degree of browning decreased by 34.43%, 36.29%, and 21.43%, respectively, whereas the brightness, rehydration ratio, total flavonoid content, and total phenol content increased by 8.94%, 16.99%, 20.57%, and 28.32%, respectively. Staged TH-IRHAD substantially reduced the drying duration, increased the efficiency, and enhanced the drying quality.