SARS-CoV 3C-like protease (3CLpro) is an attractive target for anti-SARS drug discovery and its dimerization has been extensively proved to be indispensable for enzymatic activity. However, the reason why the dissociated monomer is inactive still remains unclear due to the absence of the monomer structural information. In this study, site-directed mutagenesis result suggested that mutation of the residue Gly11 on the alpha-helix A' of domain I induced a complete activity loss of SARS-CoV 3CLpro. To further elucidate the contribution of Gly11 to 3CLpro dimerization, the crystal structure of Gly11_Ala mutant was subsequently analyzed, which reveals that mutation of Gly11 can result in the complete crystallographic dimer dissociation of SARS-CoV 3CLpro. The mutation might shorten the alpha-helix A' and cause a mis-oriented N-terminal finger that could not correctly squeeze into the pocket of another monomer during dimerization, thus destabilizing the dimer structure. In addition, several structural features essential for catalytic activity, including the catalytic dyad, the oxyanion hole, His163 and Glu166 of the S1 subsite, are severely impaired in G11A monomer. Based on the dramatic position change of domain III against the chymotrypsin fold in G11A monomer, we proposed a putative dimerization model for SARS-CoV 3CLpro. As the first reported monomer structure for SARS-CoV 3CLpro, the crystal structure of G11A mutant might hopefully provide valuable insight into the dimerization mechanism of the protease, and supply the direct structure evidence for the incompetence of the dissociated monomer.