A two-level implicit compact formulation with quasi-variable meshes is reported for solving three-dimensions second-order nonlinear parabolic partial differential equations. The new nineteen-point compact scheme exhibit fourth and second-order accuracy in space and time on a variable mesh steps and uniformly spaced mesh points. We have also developed an operator-splitting technique to implement the alternating direction implicit (ADI) scheme for computing the 3D advection-diffusion equation. Thomas algorithm computes each tri-diagonal matrix that arises from ADI steps in minimal computing time. The operator-splitting form is unconditionally stable. The improved accuracy is achieved at a lower cost of computation and storage because the spatial mesh parameters tune the mesh location according to solution values' behavior. The new method is successfully applied to the Navier-Stokes equation, advection-diffusion equation, and Burger's equation for the computational illustrations that corroborate the order, accuracies, and robustness of the new high-order implicit compact scheme. The main highlight of the present work lies in obtaining a fourth-order scheme on a quasi-variable mesh network, and its superiority over the comparable uniform meshes high-order compact scheme.