The invention discloses a method for synthesizing a CoAPO-41 molecular sieve and relates to a method for synthesizing a molecular sieve. The invention aims at solving the problems that relatively high acid site density cannot be formed without introducing a large quantity of Si atoms in the existing synthesis process of an SAPO-41 molecular sieve, but the Si atoms hardly enter the molecular sieve framework and are uniformly distributed on the framework to form a non-framework amorphous species which deposits in the pore orifices or pore channels of the molecular sieve to cause partial blocking of the pore orifices or pore channels. The method comprises the following steps: (I) preparing initial gel; and (II) crystallizing and roasting to obtain the CoAPO-41 molecular sieve. In the invention, the prepared CoAPO-41 molecular sieve is a spherical aggregate or crystal cluster consisting of nano rods, wherein the crystallizing time is only (1/2)-(1/3) of that of the prior art while mixed crystals are avoided; and the CoAPO-41 molecular sieve can be applied to the fields such as petrochemical industry as an environment-friendly acid catalyst.