This work focuses on the structural exploration of micro-sized crystals based on a well-known methanofullerene, [6,6]-phenyl-C-61-butyric acid methyl ester (PCBM). We have succeeded in producing PCBM crystals with the hexagonal symmetry through the liquid liquid interfacial precipitation (LLIP) method. We found that smaller but more regular PCBM crystals tend to form in the oversaturated PCBM solutions with solvents of lower solubility for PCBM, such as tetrahydrofuran (THF) and 1,4-dioxane. The structure of the produced crystals also shows a dependence on the solvents, which can be attributed to the incorporation of different solvent molecules into PCBM crystals. Under thermal annealing, for the first time, we have observed a crystalline to crystalline phase transformation of these hexagonal PCBM crystals. Along with the phase transformation, the morphology of the crystals has also been transformed from the hexagon to long needles. In addition, the needlelike crystals arrange themselves with a relative angle of 60 degrees to each other, which implies an intrinsic structural correlation between needlelilce and hexagonal crystals.