In this study, mycophenolic acid-nicotinamide (MPA-NAM) and mycophenolic acid-acetoguanamine (MPA-AGA) cocrystals were synthesized and characterized using single-crystal X-ray diffraction, Fourier transform spectroscopy and thermal analysis. Intrinsic intermolecular interactions were investigated through Hirshfeld surface and electrostatic potential surface analysis. The results indicated that MPA-NAM and MPA-AGA cocrystals possessed the same types of hydrogen bonds but different hydrogen bond connectivity. Thermodynamic studies revealed that MPA-NAM and MPA-AGA cocrystals exhibited incongruent dissolution behaviors in the chosen solvent. Model regression results indicate that the 1:1 complex formation existed during the dissolution of the MPA-NAM cocrystal, whereas 1:1 and 1:2 solution complexes presented in the MPA-AGA cocrystal. The complicated complexation in the MPA-AGA cocrystal induced all fragments of MPA-AGA to possess higher energies, facilitating MPA-AGA cocrystal precipitation from the solution, which was testified by Energy calculations.