Drying is a key step in starch noodle production. The effects of high temperature (60, 70, 80 °C) and high relative humidity (65%, 75%, 85%) drying (HTHD) on the moisture distribution, starch microstructure and cooking characteristics of extruded whole buckwheat noodles were investigated. Compared to the conventional hot-air drying (CHAD) at 40 °C, the increase in drying temperature (60–80 °C) and the decrease in relative humidity (85%–65%) significantly improved drying efficiency of the extruded noodles. By adjusting drying temperature and relative humidity, the rate of moisture migration in noodles and phase transition of starch could be appropriately controlled. The optimum drying parameters (T70H75, 70 °C drying temperature and 75% relative humidity) showed smooth and dense network structure, resulting in the lowest cooking loss (6.61%), broken rate (0%), highest hardness (1 695.17 g) and springiness (0.92). However, the total flavonoid content (TFC) and the total phenolic content (TPC) reduced by 6.81%–28.50% and 7.19%–53.23% in contrast to CHAD, and the color of buckwheat noodles became darker through HTHD. These findings showed the potential of HTHD for increasing drying efficiency and improving buckwheat noodle quality. The appropriate drying parameters could maintain a balanced relationship between moisture migration in noodles and phase transition of starch, which resulted in better cooking quality for extruded whole buckwheat noodles. Such a study is valuable for regulating the process conditions of buckwheat-based foods and promoting its commercial utilization.