The withholding of personal income tax is an important work of financial department in colleges and universities. The new tax law implemented in 2019 has introduced a series of measures such as special additional deductions, which make the financial department of colleges and universities face new challenges. Starting from the positive and negative effects of the new personal tax law on the macro level, this paper further analyzes the positive and negative effects of the new personal tax law on the financial department of colleges and universities, and puts forward the overall and special measures to deal with the new personal tax law and provide corresponding countermeasures and suggestions for the financial department of colleges and universities.