Arbuscular mycorrhizal fungi (AMF) are widely distributed in nature. They live in the roots of higher plants, in a symbiotic relationship. In this study, five commercial species of yams (Dioscorea spp.) were inoculated with six species of AMF, Glomus clarum, G. etunicatum, G. fasciculatum, Gigaspora sp., G. mosseae, and Acaulospora sp., in field cultivation conditions to investigate the influence of AMF inoculation on tuber weights and secondary metabolite content in yam tubers. The results showed that mycorrhizae formation rates ranged from 63.33% to 90%. G. etunicatum inoculation treatment increased the tube weights of the five species of yam tubers by 39%, 35%, 20%, 56%, and 40% for Tainung 1, Tainung 2, Ercih, Zihyuxieshu, and Tainung 5, respectively. The content of secondary metabolites, such as polyphenols, flavonoids, and anthocyanin, was significantly increased by the AMF treatment in tuber flesh and peel of all the tested yam species. Specifically, the maximums exchange of secondary metabolite contents increased to 40%, 42%, and 106% for polyphenols, flavonoids, and anthocyanin, respectively, in the tuber fresh. This study revealed that different species of yam had varying degrees of affinity with various AMF species; selecting effective AMF species is necessary to facilitate yam growth and improve the quality and quantity of yam tubers.