The cleaning agent for integrated circuit substrate silicon chip features that it consists of organic base functioning as pH regulator, complexing agent, corrosion inhibitor, dispersant and oxidizing assistant simultaneously in 40-45 %, surfactant functioning to lower surface tension of the solution, enhance mass transfer and eliminate metal ion simultaneously in 7-15 %, and water in 40-53 %. The cleaning method with the cleaning agent includes adding deionized water in 8-15 times, twice ultrasonic cleaning at 50-60deg.c for 5-10 min each, twice ultrasonic rinsing in deionized water at 50-60deg.c for 5-10 min each, sprinkling and stoving. The present invention has the advantages of excellent cleaning effect, simple preparation process, convenient operation and environment friendship.