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This study compares the predictive performance of different classes of adaptive neuro-fuzzy inference systems (ANFIS) in predicting the permeability of carbon dioxide (CO2) in mixed matrix membrane (MMM) containing the SAPO-34 zeolite. The hybrid neuro-fuzzy technique uses the MMM chemistry, pressure, and temperature to estimate CO2 permeability. Indeed, grid partitioning (GP), fuzzy C-means (FCM), and subtractive clustering (SC) strategies are used to divide the input space of ANFIS. Statistical analyses compare the performance of these strategies, and the spider graph technique selects the best one. As a result of the prediction of more than 100 experimental samples, the ANFIS with the subtractive clustering method shows better accuracy than the other classes. The hybrid optimization algorithm and cluster radius = 0.55 are the best hyperparameters of this ANFIS model. This neuro-fuzzy model predicts the experimental database with an absolute average relative deviation (AARD) of less than 3% and a correlation of determination higher than 0.995. Such an intelligent model is not only straightforward but also helps to find the best MMM chemistry and operating conditions to maximize CO2 separation.