In this paper, we extend the GKZ-system method to the more general case: compact Complete Intersection Calabi-Yau manifolds (CICY). For several one-deformation modulus compact CICYs with D-branes, the on-shell superpotentials in this paper from the extended GKZ-system method are exactly consistent with published results obtained from other methods. We further compute the off-shell superpotentials of these models. Then we obtain both the on-shell and off-shell superpotentials for several two-deformation moduli compact CICYs with D-branes by using the extended GKZ-system method. The discrete symmetrical groups, Z 2 , Z 3 and Z 4 , of the holomorphic curves wrapped by D-branes play the important roles in computing the superpotentials, in some sense, they are the quantum symmetries of these models.Furthermore, through the mirror symmetry, the Ooguri-Vafa invariants are extracted from the A-model instanton expansion.