Tea is an economic shrubby plant in tropical and subtropical regions of the world. To obtain high yield in tea cultivation, chemical fertilizer application rates have generally been used. However, a large quantity of chemical fertilizer application in a long-term continuously ratooned and monoculture tea orchard can inevitably lead to soil acidification and a decline in fertility. Therefore, the restoration of soil fertility and the sustainable development of tea planting by organic ways are critical for the tea industry. In this study, field trials were conducted in the tea orchard that was continuously ratooned and mono-cultured for 20 years. Nitrogen fertilizer (NF), Laredo soybeans green manure (LF), and goat manure (GM) treatments were applied to restore optimum acidity, soil fertility, microbial activity, and the community structure of a long-term continuously monoculture tea orchard. This paper investigated that the pH value was increased from 4.23 to 4.32 in GM and LF, respectively. Similarly, the content of exchangeable acidity (EA) was decreased by 1.21 and 1.46 cmol·kg−1 in GM and LF, respectively. Available nutrient results indicated that the content of NH4+-N was increased by 3.96, 4.38, NO3−-N by 1.07, 2.16, AP by 3.46, 6.86, AK by 0.26, 0.3 mg kg−1 in GM and LF treatments, respectively. Enzyme analysis revealed that the activity of urease and sucrase was promoted by 7.98 mg·g−1·24 h−1 and 6.77 mg·g−1·24 h−1, respectively, in LF treatment. Likewise, the activity of acid phosphatase and polyphenol oxidase was sharply increased by 2.3 mg·g−1 h−1 and 63.07 mg·g−1 h−1 in LF treatments. Additionally, the activity of urease, sucrase, acidic phosphatase, polyphenol oxidase, and peroxidase were also significantly increased by applying GM treatments. Meanwhile, LF and GM treatments significantly improved soil microbial biomass as well as low weight organic acid content in degraded tea rhizosphere. Furthermore, high throughput sequence results illustrated that the relative abundance of Rhizobiaceae and Bradyrhizobiaceae families increased in LF and GM treatments, respectively, which are mostly a kind of nitrogen fixer and plant growth promoting bacteria. Taken together, the physiological traits of the new sprouts and the biochemical components of new tea leaves were also significantly improved by GM and LF treatments. From this study, it is concluded that LF and GM are good agriculture management practices, which promote plant growth, yield, and nutrient availability by maintaining and improving pH, enhancing available nutrients status, improving the secretion of low molecular weight organic acids, and balancing the microbial community structure in the long-term mono-cultured tea orchard.