Explainable artificial intelligence (XAI) holds significant importance in enhancing the reliability and transparency of network decision-making. SHapley Additive exPlanations (SHAP) is a game-theoretic approach for network interpretation, attributing confidence to inputs features to measure their importance. However, SHAP often relies on a flawed assumption that the model’s features are independent, leading to incorrect results when dealing with correlated features. In this paper, we introduce a novel manifold-based Shapley explanation method, termed Latent SHAP. Latent SHAP transforms high-dimensional data into low-dimensional manifolds to capture correlations among features. We compute Shapley values on the data manifold and devise three distinct gradient-based mapping methods to transfer them back to the high-dimensional space. Our primary objectives include: (1) correcting misinterpretations by SHAP in certain samples; (2) addressing the challenge of feature correlations in high-dimensional data interpretation; and (3) reducing algorithmic complexity through Manifold SHAP for application in complex network interpretations. Code is available at https://github.com/Teriri1999/Latent-SHAP.