The use of rain shelters in pear cultivation has been shown to improve yields and the appearance and quality of fruit, as well as reduce diseases and pests; however, how rain shelters affect soil chemical properties, soil enzyme activity, and soil microbial diversity remains unknown. Here, we studied pear trees under rain-shelter cultivation and open-field cultivation in the same orchard and compared fruit quality, soil chemical characteristics, soil enzyme activity, and soil microbial diversity. Results showed that rain shelters can significantly (p < 0.05) increase the sugar content (sweetness) of pear fruits and decrease the content of acids. The levels of available phosphorus, available potassium, organic matter, and water in soils under rain shelters were significantly (p < 0.05) lower than in soils in open fields. Rain-shelter treatment increased soil polyphenol oxidase activity and decreased phosphomonoesterase, urease, and sucrase activity. Analysis of microbial carbon-source utilization rates and microbial diversity showed that open-field cultivation is beneficial for microbial carbon-source utilization and microbial diversity in rhizosphere soil. Our study found that rain-shelter cultivation is not beneficial to soil fertility, microbial carbon-source metabolism and utilization, matter cycling, or microbial diversity and that the use of rain shelters may require appropriate nutrient and organic matter supplementation to maintain long-term cultivation of crops; whereas, the effects of environmental factors on open-field cultivation are greater, and more refined water and fertilizer management is required to improve fruit quality.