Purpose: To observe the effect of the cavity design of the direct composite restoration on a real case of the patient’s tooth structures after applying mandibular kinematics with finite element analysis. Materials and Methods: Four complex maxillomandibular models of the maxillary right second molar and mandibular right second molar were constructed from the patient’s CBCT acquisition, and the patient’s kinematic data recorded with Modjaw were added. Different shapes and sizes of mesio-occluso-distal (MOD) composite restorations were simulated, including the polymerization shrinkage of this material. Finite element analyses were used to observe the von Mises stresses occurring during polymerization and mastication. Results: The stresses were observed at the cavity margin, and the amplitude of the stresses was higher when the enamel volume was lower. The reduction in occlusal enamel volume with the open-angle vestibular and palatal walls resulted in a greater increase in stresses observed on the structures. Conclusions: The occlusal enamel is the area that bears the maximum masticatory stress, and the loss of this enamel volume generates a much greater concentration of stress on the underlying structures. It is important to preserve as much enamel tissue as possible when designing a cavity for a direct composite restoration.