Recently, the need for manufacturing has been emphasized worldwide due to environmental problems. Machine tool parts that cause irregular damage can extend the life of existing products with low cost and materials using a laminated manufacturing process. A direct energy deposition (DED) process, which is one of the additive manufacturing processes, is advantageous in remanufacturing because a molten-pool be generated of a high energy heat source and a metal powder or a metal wire can be supplied to form a desired shape. However, in the DED process, rapid heating and cooling around the deposition region generates rapid heat history, resulting in residual stress. In this paper is to analyze the influence of deposition and substrate shapes on residual stress characteristics in the vicinity of the repaired region of parts for machine tools using a DED process and to select a groove type that can reduce stress concentration and residual stress. After that, a substrate for repairing machine tool parts is designed and manufactured in an appropriate groove shape. Three-dimensional thermo-mechanical analysis according to the groove angle and corner radius was conducted to analyze the residual stress according to the groove angle and corner radius to predict the residual stress distribution of each shape. A three-dimensional thermo-mechanical analysis according to the groove angle and deposition type was performed to predict the residual stress distribution near the repair by deposition type. Subsequently, two-dimensional finite element analysis model were produced and thermo-mechanical analysis was conducted to compare the differences with the results of three-dimensional analysis. In addition, a two-dimensional thermo-mechanical analysis according to the base groove depth and groove shape was performed to predict the residual stress distribution according to the groove depth and groove shape. A two-dimensional analysis model according to the pore position was generated and thermo-mechanical analysis was performed to predict the residual stress distribution according to the pore position. Finally, a basic experiment was conducted by determining the substrate and the deposition material, and a substrate for repairing machine tool parts was manufactured. The groove shape of the machine tool parts repair substrate is designed to be an appropriate groove shape derived from two-dimensional and three-dimensional finite element analysis. After manufacturing the sample, the deposition characteristics of the machine tool parts repair deposition were investigated through deposition type, pore, and hardness analysis.