The negative externalities of China’s commodity market segmentation have aroused public concern. At the same time, agricultural carbon emission reduction is an important part of China’s “two-carbon” target. Therefore, exploring the impact of China’s commodity market segmentation on agricultural carbon productivity can provide a useful reference for market-oriented economic development and low-carbon development of developing countries. To this end, based on the panel data of 31 provinces in China from 2004 to 2021, we analyzed the impact of Chinese commodity market segmentation on agricultural carbon productivity. The research conclusion shows that, in China, the commodity market segmentation will significantly inhibit the improvement of agricultural carbon productivity. However, in the process of this negative influence, economic development and information technology development play a positive regulatory role, which can alleviate this inhibitory influence. To this end, China should speed up the construction of a unified domestic market, constantly improve the level of economic development and information technology, reduce the segmentation of commodity markets, and improve agricultural carbon productivity.