Improvising bioceramics for enhancing their biocompatibility and physical properties has been a focus area for the dental industry. To further explore this area, this study reports a novel green synthesis and molecular in vitro biocompatibility of calcium aluminosilicate-chitosan nanohybrid (CAS-CH). The nanohybrids were synthesized by using a high energy ball milling (HEBM) technique and then characterized for their physiochemical properties using standard techniques including scanning electron microscopy (SEM) and dynamic light scattering (DLS). In vitro cytotoxicity evaluation of a synthesized nanohybrid was made with a RAW264.7 cell line using cell viability assays, such as, MTT, cellular morphology analysis, induction of oxidative stress, and apoptosis. CAS-CH nanohybrids were synthesized at three milling time points: 1H, 2H, and 3H. With increasing milling time, we found a reduction in sizes of particles and increased zeta potential. Viability of cells was found to be decreased with an increase in concentration. Moreover, toxic effects like ROS generation and apoptosis were reduced with increasing milling time. Computational and experimental analysis elucidated the mechanism of toxicity as a consequence of influential functionality of Sod1 and p53 proteins due to interaction and internalization of the nanohybrids with amino acid residues via hydrogen bonds and hydrophobic interactions. The detailed study depicted a novel way of synthesizing biocompatible bioceramic nanohybrids with a mechanistic insight of its cytotoxicity profile.