The cellulase cocktail of marine Aspergillus niger exhibited halo-tolerant and thermostable properties, which is of great potential in industrial application. In order to excavate single tolerant cellulase components from the complex cellulase cocktail, constitutive homologous expression was employed for direct obtainment of the endoglucanase (AnEGL). The constitutive expression system seems as “separation factor” to be implanted into cell for conveniently obtaining a single target enzyme. Enzymatic property study revealed that AnEGL exhibited a property of halo-tolerance and an outstanding thermostability in high salt environment. Significantly, its activity increased by 29% and the half-life at 65 °C increased by 26.7-fold with the presence of 4.5 M NaCl. Molecular dynamics (MD) simulation revealed that Na+ and Cl－ could form salt bridges with charged residues, and then influenced the activity of loops and the stability of substrate binding pocket, which accounted for the halo-tolerance and thermostability. Further, site-specific mutagenesis study proved that the residues Asp95 and Asp99 in the pocket were of great concern for the halo-tolerance and thermostability. The halo-tolerant and thermostable AnEGL was of great value in lignocellulosic utilization and the conjectural mechanisms were of referential significance for other tolerant enzymes.