With the profound integration of digital technology and traditional agriculture, the whole industry chain of rural e-commerce, as an advanced system, is reshaping the production, sales, and management models of agriculture and is emerging as a new catalyst for the advancement of digital agriculture through significant innovation. This paper focuses on the digital empowerment attributes and strategic attributes of the whole industrial chain of rural e-commerce, and evolutionary game models under market mechanisms and regulations are constructed. It examines the influence of various elements, such as the digital technology empowerment coefficient, on collaborative innovation within the whole industry chain of rural e-commerce. Using case simulations, this paper discusses the role of government regulation and intervention when market mechanisms are inadequate. The study reveals that factors such as the digital technology empowerment coefficient, technology absorptive capacity, and the amount of technology and information stored in collaborative innovation positively influence the whole industry chain. Potential risk losses and free-rider gains have negative effects on the evolution of the system toward collaborative innovation. When market mechanisms are inadequate, a combination of operational cost subsidies and incentive measures can yield more effective policy synergy, with the incentive impact of cost subsidies being particularly notable. The strategic application of enterprise-liquidated damage and government penalties will aid in regulating and directing corporate behavior. The findings of this research not only offer a new microlevel explanation for understanding the decision-making mechanism behind collaborative innovation in the whole industrial chain of rural e-commerce but also serve as a reference for government policy formulation to ensure the stability of the whole rural e-commerce industry chain.