We report the molecular beam epitaxy (MBE) growth of the manganese(II) phthalocyanine thin films with unique crystal structure and the measurement of their magnetic properties. The epitaxial films were grown on hydrogen-terminated Si(111) substrates. Reflection high energy electron diffraction observations showed that the crystal structure of the films is different from that of the bulk crystal. A large magnetic anisotropy was observed in the measurements with the SQUID magnetometer. The films did not show canted ferromagnetism which is usually observed in the beta-type crystal of manganese phthalocyanine. The magnetic susceptibility measured with magnetic field normal to the substrate obeyed the Curie-Weiss law with a negative Curie-Weiss constant, indicating the existence of the antiferromagnetic interaction. The negative Curie-Weiss constant was also observed in disordered films of manganese phthalocyanine. The variation of magnetic properties between the bulk crystal and the films is explained in terms of the difference in superexchange interaction caused by microscopic modification of the crystal structure, i.e., the stacking arrangement of the molecules.