The tax deduction of individual income tax in Japan includes two stages：the deduction of necessary expenses and the income deduction，which are deducted in the calculation of classified income and taxable income. The necessary expenses for taxpayers to obtain income，as well as the factors affecting the tax bearing capacity，such as family composition，spouse employment，physical condition，additional expenses and special matters，are comprehensively considered. On the basis of ensuring the basic life of taxpayers，the tax deduction system is designed to improve the function of income redistribution of individual income tax，and to cooperate with consumption tax and other taxes to adjust the economy as a policy tool. In recent years，with the changes of Japan’s economic and social structure，the tax deduction system of Japanese individual income tax has been revealed many problems. Discussions around improving the function as fiscal revenue and the function of income redistribution，promoting the employment diversification and female employment，and implementing the integrated reform of tax system and social security，have been carried out extensively in Japan. The design and evolution process of Japan’s personal income tax deduction system has its own characteristics but also some shortcomings.