The invention relates to a synthesis method of a heteroatom-containing ZSM-39 molecular sieve. The method comprises: mixing a silicon source, a heteroatom source, an alkali source, piperidine and water evenly into a gel, under certain temperature, subjecting the reaction mixture to hydrothermal crystallization under a self-generated pressure, and carrying out filtering, washing and drying so as to obtain a Ti, V, Cr, Fe, Co or Ni-containing heteroatom molecular sieve, the X-ray diffraction (XRD) spectrum of which has a structure of a ZSM-39 molecular sieve. The vibration frequency of an Si-O tetrahedron at the 800cm<-1> site in an infrared spectrum (IR) of the molecular sieve undergoes offset in a range of 778-813cm<-1>. The method disclosed in the invention is simple, practical and low in cost. Until now, no published report on the synthesis method of a heteroatom-containing ZSM-39 molecular sieve can be acquired.