Due to high stiffness/weight ratio, composite materials are widely used in aerospace applications such as motor case of rockets which can be regarded as a pressure vessel. The most commonly used method to manufacture pressure vessels is the wet filament winding. However, the mechanical performance of a filament wound pressure vessel directly depends on the manufacturing process, manufacturing site environmental condition, and material properties of matrix and fiber. The designed pressure vessel may not be manufactured because of the mentioned issues. Therefore, manufacturing of filament wound composite structures are based on manufacturing experience and experiment. In this study, effects of layer-by-layer thickness and fiber volume fraction variation due to manufacturing process on the mechanical performance were investigated for filament wound pressure vessel with unequal dome openings. First, the finite element model was created for designed thickness dimensions and constant material properties for all layers. Then, the model was updated. The updated finite element model considered the thickness of each layer separately and variation of fiber volume fraction between the layers. Effects of the thickness and fiber volume fraction on the stress distribution along the motor axial direction were shown. Also hydrostatic pressurization tests were performed to verify finite element analysis in terms of fiber direction strain through the motor case outer surface. Important aspects of analyzing a filament wound pressure vessel were addressed for designers.