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The multi-stream heat exchanger (MS-HEX) is an important equipment in CO2 capture processes, especially for CO2 condensation. By now, little attention has been paid to thoroughly investigating its performance. To provide insights for optimizing the design and operation of the MS-HEX, this paper evaluated the impacts of some key factors, such as the flow arrangement and the content of non-condensable (NC) gases, on the performances of the MS-HEX, including the exit vapor fraction, the pressure drop, the heat transfer coefficient (HTC), and the sub-cooling degree. A 3D CFD model was developed and validated. Based on simulations, it was found that the flow arrangement can clearly affect the performance of the MS-HEX, and there existed an optimal one, which can give the highest sub-cooling degree. Moreover, increasing the volume fraction of NC gases can lead to a decrease of the HTC and the sub-cooling degree; and Ar showed the biggest impact, followed by O2 and N2. For instance, compared to condensing a stream containing 5 vol % N2, condensing a stream containing 5 vol % Ar led to a lower HTC and a lower sub-cooling degree, which can be up to 27.3% and 4 K, respectively.