Guangxi Zhuang Autonomous Region is located in the subtropical and tropical regions of southern China, with mild temperatures and abundant natural resources. It is one of the origins of pottery in Eurasia, and potteries dating to 10000 years ago have been found in several sites. Organic residue analysis is one of the most effective methods to understand the use of pottery and the patterns of processing animal and plant resources. This method has proved to be effective in many archaeological sites in other regions, but has not been widely applied to the Guangxi region. The Fuziyan site is located at the intersection of the Li River and Xiangsi River in Guilin, Guangxi, dated to 5000~3000 BP, and it covers an area of more than 7000 m². Four kinds of cultural deposits including cave, terrace, hillside and rocky mountain have been excavated. The excavation project was carried out during 2014 and 2016 which determined three phases. Phase I dated back to ~5000 BP, Phase II to ~4000 BP and Phase III to 4000~3000 BP. The various types of decorative pottery, stone axes and many other relics unearthed in Phase III were relatively similar to the contemporaneous relics in the surrounding area, suggesting that the cultural connotation was diversified. In this study, 28 pottery sherds collected from Phase II and Phase III were analyzed by lipid extraction, gas chromatography-mass spectrometry and gas chromatography-combustion-isotope ratio mass spectrometry. The results show that the fatty acid content in each sample is higher than 5 μg/g, indicating that these pottery sherds were well-preserved and met the requirement for stable isotope analysis. Moreover, each sample contained various kinds of lipids and other biomarkers, implying the mixture of animal and plant sources. The δ¹³C value suggests possible origins from freshwater animals and wild non-ruminants. However, only a few freshwater animal biomarkers were found by GC-MS analysis. This could be due to insufficient processing temperature or other cooking methods. All of these samples obtain lipids from plants or biomarkers of plants, which indicates that those potteries were utilized in processing plants. There might be multiple ways to process different plants. The detection of citric acid suggested that potteries were used to store or cook fruits. In sum, it is speculated that people in the Fuziyan site might still rely on fishing-gathering subsistence. A comparative study with previous pottery organic residue analyses demonstrates that from the Early Neolithic period to the Shang and Zhou dynasties (12000~3000 BP), the subsistence strategy of ancient inhabitants in the Guangxi region underwent a significant diachronic transition, characterized by a shift from diversified food procurement to a more specialized dietary pattern. This trajectory reflects an evolutionary trend in resource utilization strategies across temporal dimensions.