The anisotropy caused by the fiber orientation that is inevitably generated by the flow during the injection molding of short fiber reinforced polymers, greatly influences the dimensional accuracy, the mechanical properties and other qualities of the final product. Since the filling stage of the injection molding process plays a vital role in determining the orientation of the fiber, an accurate analysis of the flow field for the filling stage becomes a necessity. Unbalanced filling occurs when a complex or a multi-cavity mold is used, leading to the development of regions where the fiber suspension is under compression. It is impossible to make an accurate calculation of the flow field during filling within analysis assuming an incompressible fluid. In this study, a FEM/FDM hybrid scheme with consideration of compressibility was developed to calculate the flow field. At the moment of complete filling, the three-dimensional fiber orientation field was estimated by solving the equation of orientation change for the second-order orientation tensor with the fourth-order Runge-Kutta method. A mold with four cavities with different filling times was produced to compare the results of numerical analysis with experimental data. There was good agreement between the experimental and theoretical results when the compressibility of the polymer melt was considered for the numerical simulation. Also, qualitative and quantitative comparisons of fiber-orientation states for compressible and incompressible fluids were made.