The invention discloses a method for synthesizing a molecular sieve containing a transition metal heteroatom LTL structure. The method is characterized by comprising the following steps: mixing a heteroatom metal source, a coordinating complexing agent, an aluminum source, potassium hydroxide, a silicon source and water according to the atomic molar ratio of (0.001-0.1): (0.1-1.0): (0.04-0.2): (0.7-1.2): 1.0: (12-50), uniformly stirring, then performing crystallization reaction at the temperature of 150-180 DEG C for 24-72h, performing suction filtration and washing on a reaction solution, and then drying at the temperature of 100-200 DEG C to prepare a product, namely the molecular sieve containing the transition metal heteroatom LTL structure. Compared with the prior art, the method has the advantages of simple process, a variety of applicable heteroatom metals, extensive raw material sources and low cost, and can better solve the difficult problem of precipitation of a heteroatom transition metal source under strong alkaline conditions, thereby being a preparation process for synthesizing the molecular sieve containing the transition metal heteroatom LTL structure, which is easy to realize industrial implementation, mild in reaction conditions and environment-friendly.