The purchasing decisions of consumers increasingly incorporate considerations of freshness and the carbon footprint of agri-foods. This study aims to investigate the impact of consumer preferences on decision-making behavior within dual-channel supply chains. Specifically, it classifies the structure of the supply chain channels into two types: producer-led and seller-led online channels, and examines two distinct decision-making scenarios: centralized and decentralized decision-making. The study applies the game theory modeling method to analyze the differences in the selling prices, freshness, low carbon levels, and profits of agri-foods in these scenarios. The findings indicate that as consumer preference for the online channel grows, it becomes more challenging to sell homogeneous agri-foods at higher prices through physical (entity) channels. Moreover, the introduction of online channels by sellers leads to higher selling prices for agri-foods in the supply chain under decentralized decision-making compared to centralized decision-making, and the freshness and low carbon level of agri-foods primarily depend on the cost structure of the supply chain. From the perspective of enhancing produce quality, promoting low carbon development, and attaining high-quality products at a reasonable price, centralized decision-making within the supply chain and seller-led online channels are more advantageous. However, it is important to note that pursuing these benefits may result in a certain amount of sacrifice in terms of supply chain profit.