Abstract: Combined with the reality of 3D FEM analyze of complicated seepage field of underground engineering,penetrability tensor is utilized to simulate the non-isotropy medium,improved abandon-element method is utilized to calculate the free surface,latent complex-material element is utilized to simulate the waterproof,slot instead of well curtain is utilized to simulate the drainage.Based on the above theory,3D FEM calculation program for seepage analyse is compiled.Finally this program is applied on seepage analysis of 2nd Project of Manwan Underground Plant.Based on the result,the factors influencing seepage flow area are analyzed.The result testifies the rationality and practicability of the program.