The low-carbon optimization of tolerance allocation involves reducing production costs and carbon emissions, while ensuring dimensional precision, making it a crucial pathway to achieving low-carbon manufacturing. However, the complex mapping mechanism between tolerance, cost, and carbon emissions makes it challenging to construct effective mechanistic models. This complexity arises from both the forward constraints of multiple-coupled design features of components and backward constraints on the differentiated processing conditions of an enterprise. Therefore, a low-carbon optimization method for tolerance allocation based on surrogate models is proposed. Firstly, the RReliefF algorithm is utilized to analyze the influence of design features and enterprise processing condition factors on the low-carbon performance of tolerance allocation, identifying key influencing factors. Secondly, a convolutional neural network (CNN)-based surrogate model is established to predict the low-carbon performance of tolerance allocation. Specifically, datasets of tolerance, manufacturing costs, and carbon emissions under different design feature constraints are constructed. To improve the training efficiency and accuracy of the prediction model, the heterogeneous data of design features are processed using the one-hot encoding technique. Subsequently, the mapping relationship between tolerance, cost, and carbon emissions is established based on the CNN. Finally, with the aim of minimizing costs and carbon emissions, a low-carbon optimization method for tolerance allocation is established based on the surrogate model and the product size chain. The convolutional neural network-Harris Hawk optimization algorithm (CNN-HHO) is utilized to generate tolerance allocation schemes that minimize both cost and carbon emissions while satisfying dimensional precision. Through a series of multi-peak test functions and practical case studies of the overrunning clutch, the results indicate that the proposed CNN-HHO algorithm demonstrates exceptional accuracy and stability in the validation on the test functions. Furthermore, the optimized overrunning clutch solution achieves approximately 2.61% cost reduction and 2.63% decrease in carbon emissions, providing further support for the effectiveness of the proposed method.