In this paper, we give a direct method to study the isochronous centers on center manifolds of three dimensional polynomial differential systems. Firstly, the isochronous constants of the three dimensional system are defined and its recursive formulas are given. The conditions of the isochronous center are determined by the computation of isochronous constants in which it doesnt need compute center manifolds of three dimensional systems. Then the isochronous center conditions of two specific systems are discussed as the applications of our method. The method is an extension and development of the formal series method for the fine focus of planar differential systems and also readily done with using computer algebra system such as Mathematica or Maple.
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