Privacy-preserving distributed distribution comparison measures the distance between the distributions whose data are scattered across different agents in a distributed system and cannot be shared among the agents. In this study, we propose a novel decentralized entropic optimal transport (EOT) method, which provides a privacy-preserving and communication-efficient solution to this problem with theoretical guarantees. In particular, we design a mini-batch randomized block-coordinate descent (MRBCD) scheme to optimize the decentralized EOT distance in its dual form. The dual variables are scattered across different agents and updated locally and iteratively with limited communications among partial agents. The kernel matrix involved in the gradients of the dual variables is estimated by a distributed kernel approximation method, and each agent only needs to approximate and store a sub-kernel matrix by one-shot communication and without sharing raw data. We analyze our method's communication complexity and provide a theoretical bound for the approximation error caused by the convergence error, the approximated kernel, and the mismatch between the storage and communication protocols. Experiments on synthetic data and real-world distributed domain adaptation tasks demonstrate the effectiveness of our method.