The invention provides a preparation method of a composite molecular sieve and application of the composite molecular sieve prepared by the method. The method includes: a. mixing a template agent, a silicon source, an aluminum source, a phosphorus source, water, a SAPO-5 molecular sieve and a SAPO-34 molecular sieve to obtain an initial gel; b. ageing the initial gel obtained in step a; and c. crystallizing the aged gel obtained in step b to obtain a crystallization product. The method for preparation of the SAPO-5/SAPO-34 composite molecular sieve provided by the invention can control the content of SAPO-34 molecular sieve at 40%-60%, and when the prepared composite molecular sieve is used for conversion of an organic oxygenated compound to low-carbon olefins, the propylene and butylene product selectivity is high, and the coke yield is low.