Exogenous selenium (Se) application into the soil is an efficient way to improve Se-enriched green tea production in Se-deficient areas, combined with a microbe-assisted strategy. This study aimed to explore the effects of Bacillus amyloliquefaciens, a popular biofertilizer, and exogenous Se application on the spring tea quality and Se content. A pot experiment with four treatments, no fertilization (Control), B. amyloliquefaciens application (BA), selenite fertilization (Se), and combined application of B. amyloliquefaciens and selenite fertilizer (BA + Se) was conducted in this study. Results showed that compared with control, 1) BA treatment significantly increased Se content in tea leaves by 57.0%. The BA treatment improved spring tea quality by reducing the ratio of tea polyphenols to amino acid (TP/AA), and the contents of total carotenoids and polyphenols, but increasing the contents of chlorophyll b, soluble sugar, caffeine, flavonoids, and L-theanine (L-The) in tea leaves. Meanwhile, the BA treatment improved soil fertility by increasing available nitrogen and available potassium in soils. 2) Se treatment significantly increased Se content in tea leaves by 6.5 times and also increased chlorophyll a, chlorophyll b, total carotenoids, caffeine, total catechins, flavonoids, polyphenols, L-The levels in tea leaves, and TP/AA. 3) BA + Se treatment significantly increased Se content in tea leaves by 5.8 times compared with control, and significantly increased soil available Se content by 59.1% compared with Se treatment. Thus, both B. amyloliquefaciens and selenite fertilizer application alone could improve tea quality. Our study highlights the great potential of B. amyloliquefaciens in Se biofortification in tea tree cultivation.