The invention relates to a sulfur-resistant and water-resistant low-temperature denitration composite molecular sieve catalyst and a preparation method thereof. The catalyst is prepared by an impregnation method, a chabasite molecular sieve H-SAPO-34 serves as a support, an active component is a composite oxide of transition metal Cu and Mn, an additive is one of Ce, Fe, Co, Mo and Cr, the supported weight of a copper element and a manganese element in the active component is 2%-10% in weight percentage, and the supported weight of additive is 1-10% in weight percentage. Compared with a Cu or Mn-based catalyst of a single component, the denitration composite molecular sieve catalyst remarkably improves denitration efficiency and heat stability by the aid of multi-metal synergistic effect, an active temperature window of the catalyst is effectively widened, and the catalyst has good sulfur resistance.