Nipah henipavirus is an emerging RNA virus with high mortality threatening global security. In South and Southeast Asia, the Nipah virus has caused numerous disease outbreaks. The matrix protein in Nipah henipavirus has an important role, in linking the viral envelope with the virus core. For virus assembly, linking the viral envelope with the virus core is very crucial. Through functional and structural explanation evaluations, bioinformatics strategies can help us better understanding the protein. This investigation aims to allocate the structural and functional annotation of protein. Moreover, the investigation attributes physicochemical parameters, three-dimensional structure, and functional annotation of the protein (QBQ56721.1) applying an in silico perspective. The in silico analysis confirmed the protein hydrophilic nature, with a secondary structure dominated by alpha (α) helices. Based on several quality assessment methodologies, the tertiary structure model of the protein has been shown to be reasonably consistent. The functional explanation suggested the protein as a structural protein connected to the viral envelope with the virus core, a protein required for virus assembly. This investigation unleashes the significance of the matrix protein (QBQ56721.1) as a functional protein required for Nipah henipavirus.