The knowledge-based human capital, low-end value chain, and total factor productivity is measured from 1996 to 2015 in Guangxi. The regression analysis is used to study the impact of knowledge-based human capital and the low-end value chain on total factor productivity. TFP of Guangxi shows a "two-stage" leap feature. Knowledge-based human capital shows a “two ladder” growth trend and has a significant positive effect on total factor productivity. The low-end value chain shows a “U” trend, and the impact on total factor productivity is inverted “U”. Further research find that the China-ASEAN Free Trade Area has a positive effect on the growth of total factor productivity in Guangxi, but it is not significant. Finally, related countermeasures and suggestions are proposed.