Archaeological evidence indicates that millet and rice spread into southwestern China successively from the Ganqing Region and the Yangtze River Valley by approximately 5000 BP. After that, southwestern China showed a diverse pattern of mixed millet–rice cultivation. As a cultural intersection, the Liangshan region was influenced by many different areas, including the Zangyi Corridor, the Chengdu Plain, and the northern Yun-Gui Plateau. Due to poor preservation conditions, little isotopic research on the human palaeodietary pattern has been conducted in the Neolithic Liangshan area. This article presents an isotopic analysis of human skeletal remains from the Houzidong site, located in the southern part of the Liangshan region, to investigate the human subsistence strategy of the site. A total of 35 isotopic data were successfully obtained from the 89 samples of this experiment, with a wide range of δ13C values (−17.4‰ to −11.5‰; −13.6 ± 1.4‰) and δ15N values (+8.6‰ to +12.0‰; +9.5 ± 0.7‰). The analysis showed that the human diet at the Houzidong site included both C3 and C4 foods, and there were diverse human subsistence strategies, based on the fact that millet would have made a significant contribution to the human diet at this site (including both millet and millet-based animals). It is hypothesized that millet agriculture in the Liangshan region may have been the result of interaction between the natural environment and the local population represented by the archaeological culture.