The protection of taxpayers’ rights fundamentally depends on the state’s ability to extract and allocate the overall financial resources. From the perspective of modern finance, taxpayers’ rights are faced with the dual problems of the insufficient and unequal protection. The former is mainly manifested in the inadequate legal regulation of administrative fees and government funds, which leads to the overburden of taxpayers’ non-tax burden; the latter is mainly manifested in the fact that taxpayers are unable to obtain “equal treatment” of state finance in public services. With the implementation of the principle of statutory taxation, the protection of taxpayers’ rights at the legislative level has made remarkable progress, but the judicial protection has refused to go further. In order to enhance the protection of taxpayers’ rights, firstly, the non-tax financing instruments of governments should be restricted; secondly, the protection of taxpayers’ rights should be equalized by guaranteeing and improving people’s livelihood and implementing fiscal preferences fairly; thirdly, the taxpayer litigation system should be improved to strengthen judicial protection.