Wencheng waxy yam is famous for its glutinous and resilient taste, similar to waxy rice, but there is currently a lack of systematic research on the quality of this featured product, and little is known about its pesticide residues. We carried out a 2-year investigation of Wencheng waxy yam at seven sites from 2021 to 2022 to determine the oxidase content and phytochemical characteristics, namely amylose, amylopectin, protein, reducing sugar, and mineral contents such as K, Fe, and Zn, , including the status of pesticide residues. The results showed that oxidase content was affected by rainfall, and adequate water reduced the production of oxidase, including polyphenol oxidase (PPO), peroxidase (POD), and superoxide dismutase (SOD), during the late growth stage of waxy yam, which was beneficial for reducing browning in yam processing. Radar map analysis showed that, with comprehensive evaluation, standardized production sites 1 and 2 had a relatively higher quality than 3–7 with small farmers. The results of pesticide multi-residue testing showed that no pesticides were detected in 64.29% samples, and the detected residues samples were very low, making the consumption of yam safe for consumers. These findings could be beneficial for the exploitation of the health benefits of waxy yam tubers and the innovation of yam-based functional products.