The colloidal crystals of polystyrene (PS) spheres were assembled from the emulsion of PS by an in situ solvent evaporation method. The local internal 3D structure of the fabricated colloidal crystals was noninvasively characterized with synchrotron radiation phase-contrast computed tomography. The satisfactory contrast difference was obtained and the shapes of the spheres were clearly reconstructed. Based on the slice images, the two-stage mechanism of crystallization process for in situ evaporation was suggested. In the initial stage, stable nucleation and growth result in formation of an ordered face-centered cubic structure with the sphere volume fraction 70.2%, which is very close to the maximum sphere packing volume fraction 74%. In the second stage, the sphere concentration in suspension decreased too much to support an adequate sphere transfer through the solvent flux to the growth front. The transformation from square to hexagonal lattice did not therefore complete under the same evaporation rate. This incompleteness results in formation of local ordered structure with randomly arranged hexagonal and square packing with a slightly low volume fraction of 68.41%.