Ab initio molecular orbital (MO) calculations have been carried out for clusters of 3,9-dinitro-5a,6,11a,12-tetrahydro [1,4] benzoxazino[3,2-b][1,4] benzoxazine (DNBB) in order to elucidate the intermolecular interactions and electronic polarizations in its monoclinic crystal with Cc (No. 9) space symmetry. There reliability of the calculated results at the Hartree-Fock (HF) SCF MO level has been confirmed comparing with those of the ab initio MP4 method in the case of a simple model of the nitromethane-ammonia system. The HF SCF MO calculations of DNBB clusters by the use of STO-3G basis set have elucidated that two different intermolecular hydrogen (H) bonding interactions are operative in the clusters extended over the unit cells, which are referred to as the alpha- and beta-types, respectively, whereas weak dispersion forces are conceivable for stabilization of the clusters within the crystallographic unit cell. According to the STO-3G calculations of the clusters, the alpha-type H bond is about 1.5 times stronger than the beta-type. It is found that molecular deformation of DNBB losing C-2 symmetry in the crystalline state can be interpreted by the difference of strength between these H bonds. The calculated results reasonably explain a morphological property on the crystal growth reported previously. The MO calculations also reveal that electronic polarizations of DNBB are considerably enhanced by intermolecular charge-transfer (CT) interactions through H bonds. In this sense the H bonds play an important role in the nonlinear optical response of the DNBB crystal. Implications of the calculated results are discussed in relation to molecular engineering approach to nonlinear optical materials.