The digital economy has brought new opportunities and new challenges to the development of agriculture and rural areas. The dislocation distribution of the supply and demand entities of the digital economy across urban and rural areas and across regions has resulted in the imbalance of tax distribution between urban and rural areas and regions. Digital economic transaction activities have a partial substitution effect on traditional economic activities, eroding the original taxation basis of rural and underdeveloped areas, and then generating a siphon effect on taxation, which damages the tax benefits of rural and underdeveloped areas. Currently, the European Union, the United States and other developed countries and regions are exploring ways to adjust the taxation mechanism to promote the coordinated development of the inter-regional digital economy, providing some lessons for China to learn from. In the future, China needs to build a tax system compatible with the digital economy, establish a sound tax distribution mechanism based on the destination principle, strengthen the digital collection and management capabilities of tax authorities in rural and underdeveloped areas, and ensure the implementation of the destination taxation principle, further play the role of digital platforms in tax allocation, use information technology to promote industrial development, expand the tax base in rural and underdeveloped areas, and promote a more fair and reasonable tax distribution in the digital economy.