Considerable amounts of amendments have been applied to remediate heavy metal-contaminated soils, but little information is available on the vertical migration of total and available heavy metals during long term immobilization with amendments. In this study, soils at the depths of 0-13, 13-30 and 30-50 cm were collected under the different dosages of apatite and lime, and the vertical migration of total Cu and Cd and their availability were investigated. Results showed that the applications of apatite and lime significantly decreased the exchangeable acid and aluminum in 0-13 cm soil and increased total Ca, and apatite application enhanced the contents of total and available Pin soils. With the increase of the dosages of apatite and lime, pH and total Cu and Cd contents in 0-13 cm soil increased gradually, but the total Cu and Cd contents in 13-30 and 30-50 cm soils decreased. Available Cu and Cd at three depths all decreased with increasing the dosages of apatite and lime. Available Cu decreased by 85.1% and 92.0% in 23.2 g/kg apatite and 4 g/kg lime amended soils, and available Cd decreased by 18.0% and 23.5%, respectively. Correlation analysis indicated that soil pH and total Cu and Cd were the main factors influenced the available Cu and Cd. In summary, the applications of apatite and lime can effectively immobilize Cu and Cd in the topsoil and reduce Cu and Cd availability and leaching downward.