Drying is an important pre-processing step in the application of Ginkgo biloba seeds powders in the food and pharmaceutical industries. Herein, the effects of sun drying (SD), freeze drying (FD), hot-air drying (HD) and vacuum drying (VD) with different temperature (50 degrees C, 60 degrees C, and 70 degrees C) on the color, proteins, key functional compounds (vitamin C and total flavonoids), and antioxidant properties of G. biloba seeds were investigated. Principal component analysis (PCA) was performed to analyze the differences in dried G. biloba seeds under different drying conditions and temperatures based on the above indexes. The effects of different drying methods on the quality of G. biloba seeds are as follows: SD > HD > VD > FD. PCA revealed that drying methods, time, and temperature have significant effects on the quality of G. biloba seeds After FD treatment, G. biloba seeds powders showed brighter color, highest protein (12.03 g/100 g), vitamin C (500.11 mu g/g), and total flavonoid (2.33 mg/g) content; and highest antioxidant capacity. VD treatment at different temperatures preserve 84.11-86.63%, 77.95-86.98% and 79.83-87.12% of protein, vitamin C, and total flavonoid in dried G. biloba seeds compared to FD treatment. Higher antioxidant capacity of dried G. biloba seeds was also found in VD treatments compared to SD and HD. The application of VD treatment is beneficial to save costs and obtain high-quality G. biloba seeds compared to FD treatment.