Abstract: This study aims to explore the effect of amelioration measures on the facility agriculture soil, as well as the physical and chemical properties of tomatoes grown through facility agriculture. The most suitable amelioration was then screened for the local degraded soils. The study site was also chosen as the greenhouse of Qinxi vegetable planting demonstration garden, Taibai County, Shaanxi Province, China. The soil samples were collected from the greenhouse, where tomato fruits were used as research materials. Three soil ameliorants were selected, including plant ash, biochar, and EM fungi. Seven treatments were then combined, including EM fungi (E), biochar (S), biochar + EM fungi (SE), plant ash (C), plant ash + biochar, plant ash + biochar + EM fungi (CSE), and the control treatment (CK). The results indicated that the seven treatments improved the physical and chemical properties of soil, where the CSE treatment performed the most, compared with the CK. Specifically, the CSE treatment significantly increased the soil pH, organic matter, total nitrogen, alkali nitrogen, total phosphorous, available phosphorous, total potassium, and available potassium by 23.06%, 130.94%, 44.34%, 52.78%, 67.72%, 127.35%, 16.24%, and 119.48%, respectively. In tomato fruits, the combined application of ameliorants was much more significant than the singular in increasing the total nitrogen of the whole plant, where the CSE treatment increased the most by 25.16%, compared with CK. A similar effect was also observed in the total phosphorous of the tomato plant, where the CSE treatment presented 2.09 folds higher than that of CK. In the total potassium of the tomato plant, the rest five ameliorant treatments except for E treatment significantly increased the total potassium, where the CSE treatment presented 1.44 folds higher than that of CK. Additionally, there was only a little effect of ameliorant application on plant ash. However, the sugar/acid ratio of tomato increased significantly, where the CSE treatment increased by 69.3%, compared with the CK. Correspondingly, there was a positive effect of soil ameliorants on soil fertility. The soil integrated fertility index of each treatment showed that the soil ameliorant increased the soil fertility, compared with the CK, where the CSE was observed with the best effect to improve the soil fertility. The highest integrated score in the principal analysis was also achieved in the CSE treatment, compared with the rest treatments. Consequently, the simultaneous application of plant ash, biochar, and EM fungi can be expected to effectively mitigate the soil acidification for better soil fertility and tomato quality of alpine facility agriculture in the study area. The finding can provide a promising way to improve the soil fertility of facility agriculture, thereby optimizing effective measures for the remediation of degraded soil.