Emission control devices such as selective catalytic reduction (SCR), exhaust gas recirculation (EGR), and scrubbers were installed in the compression ignition (CI) engine, and flow analysis of intake air and exhaust gas was required to predict the performance of the CI engine and emission control devices. In order to analyze such gas flow, it was inefficient to comprehensively analyze the engine’s cylinder and intake/exhaust systems because it takes a lot of computation time. Therefore, there is a need for a method that can quickly calculate the gas flow of the CI engine in order to shorten the development process of emission control devices. It can be efficient and quickly calculated if only the parts that require detailed observation among the intake/exhaust gas flow of the CI engine are analyzed in a 3D approach and the rest are analyzed in a 1D approach. In this study, an algorithm for gas flow analysis was developed by coupling 1D and 3D in the valve systems and comparing with experimental results for validation. Analyzing the intake/exhaust gas flow of the CI engine in a 3D approach took about 7 days for computation, but using the developed 1D–3D coupling algorithm, it could be computed within 30 min. Compared with the experimental results, the exhaust pipe pressure occurred an error within 1.80%, confirming the accuracy and it was possible to observe the detailed flow by showing the contour results for the part analyzed in the 3D zone. As a result, it was possible to accurately and quickly calculate the gas flow of the CI engine using the 1D–3D coupling algorithm applied to the valve system, and it was expected that it can be used to shorten the process for analyzing emission control devices, including predicting the performance of the CI engine.