It is notable that the adoption of GM glyphosate-tolerant crops increases glyphosate use but reduces non-glyphosate herbicide use; and adoption of GM insect-resistant crops significantly reduces insecticide use. While the health hazard of pesticide use has been well documented, little literature evaluates the health effects of different pesticides related to GM crops in an integrated framework. This study aims to associate the uses of different pesticides related to GM crops with the blood chemistry panel and peripheral nerve conduction of Chinese farmers. Pesticides used by farmers were recorded and classified as glyphosate, non-glyphosate herbicides, chemical lepidopteran insecticides, biological lepidopteran insecticides, non-lepidopteran insecticides and fungicides. The multivariate regression results show that none of the examined 35 health indicators was associated with glyphosate use, while the use of non-glyphosate herbicides was likely to induce renal dysfunction and decrease of serum folic acid. The use of chemical lepidopteran insecticides might be associated with hepatic dysfunction, serum glucose elevation, inflammation and even severe nerve damage. In this context, if GM crops are adopted, the alterations in pesticide use may benefit farmer health in China and globe, which has positive implications for the development of GM crops.