Stark levels and EPR parameters of Er3+ doped in Bi4Ge3O12 crystal were studied by diagonalizing 364×364 complete energy matrices. Simultaneously, the crystal-field and J-J mixing effects on the EPR g-factors from the higher lying manifolds were evaluated, quantitatively. The results indicate that the dominant J-J mixing contribution from manifold 2K15/2 accounts for about 2.5% for the Er3+. However, the most significant high-order mixing effect is from the crystal-field admixture between the first excited manifold 4I13/2 and ground manifold 4I15/2, where the contribution to g⊥ is almost twice as much as that to g// (0.21% for g⊥, 0.092% for g//).The other crystal-field and J-J mixing effects from the higher lying manifolds can be neglected. Therefore, only considering the contribution of ground manifold 4I15/2 to EPR g-factor is a good approximation for the complex system doped with Er3+ ions.