The invention relates to a preparation method of microstructure graphite. The preparation method comprises the following steps: adopting superfine particle pitch cokes as aggregates and high-softening point asphalt as a bonding agent, preparing a paste material in a manner of liquid phase dispersion mixing and crushing to prepare pressed powder; preparing isotropic graphite with compact microstructure and small pore size distribution through isostatic press molding, carbonization, impregnation and high-temperature graphitization. The preparation method provided by the invention has the advantages that with the adoption of a raw material uniform blending process, on one hand, interfacial bonding of aggregate carbon and bonding agent bitumen is improved, and on the other hand, the agglomeration and non-uniform dispersion of the superfine particle isostatic pressure graphite are avoided, so that the possibility of occurrence of heat treatment cracking phenomenon is greatly reduced, and a favorable technical support is provided for the preparation of the superfine particle isostatic pressure graphite with large size. Moreover, the preparation method is wide in raw material source, lower in cost, simple in process and easy for large-scale batch production.