The invention relates to a method for preparing a high-content double-transition metal heteroatom composite molecular sieve. By using a stepwise synthesis method, a a MFI primary structure is firstly synthesized; then a M1-MFI molecular sieve is taken as part of silicon sources wherein M1 is one or two selected from the group consisting of Ni, Co, Cu, Fe, Zn, Cr and the like; M1-MFI is introduced into the hole wall of a mesoporous M2-MCM-41 molecular sieve wherein M2 is one or two selected from the group consisting of Ni, Co, Cu, Fe, Zn, Cr and the like; amorphous substances are guided to arrange in order to change defects of amorphous hole wall of the mesoporous molecular sieve, increase the wall thickness and raise heat stability and hydro-thermal stability of the mesoporous M2-MCM-41 molecular sieve. In the mean time, ion association complex formed by the interaction between a traditional template and a metal coordination compound is taken as a template of the synthesis molecular sieve, and metal ion is directly introduced into the molecular sieve skeleton through the template, successfully designing and synthesizing the double-transition metal heteroatom composite molecular sieve. The above composite molecular sieve material has well-regulated crystal structure, high metal content, two uniform mesoporous apertures, large specific surface area and pore volume, and good heat stability and hydro-thermal stability.