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Fair clustering aims to divide data into distinct clusters while preventing sensitive attributes (\textit{e.g.}, gender, race, RNA sequencing technique) from dominating the clustering. Although a number of works have been conducted and achieved huge success recently, most of them are heuristical, and there lacks a unified theory for algorithm design. In this work, we fill this blank by developing a mutual information theory for deep fair clustering and accordingly designing a novel algorithm, dubbed FCMI. In brief, through maximizing and minimizing mutual information, FCMI is designed to achieve four characteristics highly expected by deep fair clustering, \textit{i.e.}, compact, balanced, and fair clusters, as well as informative features. Besides the contributions to theory and algorithm, another contribution of this work is proposing a novel fair clustering metric built upon information theory as well. Unlike existing evaluation metrics, our metric measures the clustering quality and fairness as a whole instead of separate manner. To verify the effectiveness of the proposed FCMI, we conduct experiments on six benchmarks including a single-cell RNA-seq atlas compared with 11 state-of-the-art methods in terms of five metrics. The code could be accessed from \url{ https://pengxi.me}.