Based on the principles and methods of system dynamics, a dynamic model for the collaborative development of rural e-commerce and digital villages has thus been constructed, revealing the feedback mechanisms between the two systems. Based on the rural economic development statistical data of Changsha City from 2015 to 2023, a simulation has been made of the impacts of factors such as investment, market demand, and technology policies. The results show that the combined multi-factor mixed strategy (Strategy 3) exhibits the most significant positive effect, followed by the strategy of strengthening market and technology guidance (Strategy 2), while the government digital investment strategy (Strategy 1) is characterized with the lowest effect. Compared to strategy 1, strategies 2 and 3 have increased the promotion of the total output value of rural e-commerce by 10.56% and 19.93%, respectively. The key to achieving high-quality collaborative development between rural e-commerce and digital rural areas lies in the decision-making of the government, which needs to find a balance between investment strategies and policy guidance, increase investment and subsidies in rural areas so as to build a comprehensive policy support system. In addition, it is recommended to implement a phased overall strategy to promote the high-quality development of rural e-commerce and digital rural areas.