Protected cultivation is the sustainable approach to horticultural crop production under adverse climates. In this study, the performance of yard-long beans under three protected cultivations, including single-span polyhouse (SSP), five-span polyhouse (FSP), and insect-proof net house (IPN), is examined and compared to open field cultivation. The above protected cultivation can extend the harvest period of pods by 6–10 days, improve their quality, and increase yield by 15.6% to 25.1%, reducing the incidence and severity of thrips and Cercospora leaf spot, rust, and powdery mildew. Among them, yard-long beans grown in SSP are longer and straighter in shape and have the lowest incidence and severity of pests and diseases and the highest levels of total polyphenols, total sugar, soluble protein, starch, and fiber. This indicates that protected cultivation has broad application in the production of yard-long beans. Through full subset regression analysis (FSRA), we report here that the yield and of yard-long bean occurrences of pests and diseases were highly impacted by climatic factors, especially UV radiation intensity and air temperature. These results have considerable implications for improving pod yield and quality and green prevention and control of pests and diseases through optimizing facility structure and fertilizer management.