Accidents involving crankshaft of marine diesel engine have recently become common. Therefore, adequate fatigue assessment of the crankshaft is required to reduce the occurrence of severe accidents. This study aims to analyze stress and deformation using actual accident cases and data, based on finite element analysis. Three-dimensional models of the crank and crankshaft were designed and developed using “Autodesk inventor.” This study identifies vulnerable areas where stress is concentrated and proposes improvement design and factor level. Using “Ansys workbench and Autodesk Nastran,” finite element analysis was performed by “static and transient structural analyses,” which were used to determine the maximum equivalent stress and total deformation at vulnerable parts of the crankshaft. The model was tested under static and dynamic loading conditions to determine vulnerable fatigue area, deformation, equivalent alternating stress, and damage using the fatigue tool. To improve the accuracy of the durability fatigue limit, fatigue analysis was also performed using the physical properties of the material applied to the model ship, with the same stiffness and heat treatment (SCM440). The simulation was conducted under the same design and similar conditions as the ship where the actual accident occurred, and excessive deformation and stress concentration were confirmed in the crank pin fillet and journal fillet parts of the crankshaft. Structural and fatigue analysis on the additional processed design model by the fillet unit confirmed that stress and deformation in the same location were reduced.