Abstract: Taking the establishment of anti-counterfeiting system as the research object, the decision-making mechanism of anti-counterfeiting investment of brand manufacturers and platform sellers in the supply chain is studied. According to the platform resale mode and agent mode respectively, the decision-making of anti-counterfeiting technology investment of product brand and platform seller is established, and the balanced anti-counterfeiting credibility, balanced anti-counterfeiting investment threshold and equilibrium profit are drawn from different channel modes, and a comparative analysis is carried out. The study finds that when the anti-counterfeiting system is established, there is always a value range of the agent fee ratio in the agent mode so that the brand and platform profit is higher than the profit in the resale mode, and at the same time, the profit of the brand in the two modes after the establishment of the anti-counterfeiting traceability mechanism is always better than the profit when the anti-counterfeiting system is not established, and the profit of the platform can be higher than the profit before the establishment of the anti-counterfeiting system under the double limit of the penetration rate and quality difference of the platform. The study also shows that under certain conditions, the selection of anti-counterfeiting traceability mechanism can improve the total profit of the supply chain.