(1) Objective: Greenhouse workers are considered a special occupational group who are exposed to more toxic and harmful substances than ordinary farmers. The health problem of this group is a public health problem that warrants attention. Taking greenhouse workers in Ningxia, China, as the research sample, this study analyzed the health risk to practitioners posed by the greenhouse working environment. (2) Method: To analyze the relationship between pesticide exposure and the health of greenhouse workers, the genetic matching method was used to exclude the influence of covariates on the results. (3) Results: The results showed a statistical significance regarding the prevalence of cardiovascular diseases (CVD), skeletal muscle system diseases (SMSD) and digestive diseases between the different exposure groups. Researching the disease symptoms found that different levels of exposure to pesticides in greenhouses could cause multisystem and multisymptom discomfort. In addition to some irritant symptoms such as eye itching, itching, and sneezing, there were also differences in terms of the frequency of discomfort such as back pain, a decline in sleep quality, memory loss, joint pain, swelling and weakness, upper abdominal pain and flatulence, in the different exposure groups. (4) Conclusion: Different levels of exposure to pesticides in greenhouses may be one of the risk factors for practitioners to suffer from various systemic diseases, affecting their health and work efficiency. This hazard is manifested not only in some acute irritant symptoms but also in chronic diseases due to long-term exposure.