The gene M6A coding a novel cold-adapt endoglucanase was cloned from Microbacterium kitamiense Sa12 isolated from a wasteland in Saga, Qinghai-Tibetan Plateau. The deduced protein sequence encoded a 411-residue polypeptide sharing similar identities with glycosyl hydrolase family 6 enzymes. The recombinant M6A displayed maximum hydrolysis activity of 1.51 U/mg toward soluble cellulose substrate, CMC at 35°C and pH 5.0, and the Km and Vmax value were 2.12 mg/mL and 15.33 μmol/min*mg, respectively. Interestingly, M6A exhibited significant activity even at ice cold condition, showing 30–40% relative activity at 0–5°C, and had good tolerance to Li+, K+, NH4+, Rb+, Ca2+, Mg2+ Zn2+, Mn2+, and Ni2+, expect divalent cation Cu2+ led to 30% residual activity. These properties might make M6A to be a promising candidate used in the psychrophilic industrial process and/ or the volatile and thermosensitive manufacturing process.