Wild boars (Sus scrofa) are extremely common in southern of China, but little study has reported dietary habits of wild boars using high-throughput sequencing technology. Due to the difficulty in obtaining samples of the stomach contents of wild boars, there are few reports on the diet of wild boars especially in karst areas. In our study, the stomach contents of 14 south China wild boars were analyzed by 16S rRNA high-throughput sequencing technology. The results showed that there were 153 genera, 93 families, and 48 orders, of which 78% were plants. Main plants food component of wild boar were Cissus, Dioscorea, Quercus, Actinidia and Houttuynia. The remaining 21% was animal food sources. It is noteworthy that Elaphodus cephalophus were detected in most of stomach samples, accounted for a large part of animal food sources. Predation of Elaphodus cephalophus by wild boars could cause a series of unforeseen problems, especially if this ongoing issue continues in the future. Our study revealed the dietary preference of wild boars under the special forest vegetation conditions in the mountainous area of southwest China, and the relationship between the diet habits of wild boars and their habitats from the perspective of resource utilization, thus providing a key scientific basis for the prevention and control of wild boars and resource protection.