The invention relates to a microporous composite silicon aluminum molecular sieve and a preparation method thereof. The method is as below: adding an inorganic alkali source into deionized water, stirring for dissolving, adding an aluminum source and a template agent to prepare an operating fluid A; adding a silicon source into the operating fluid A to obtain a silicon aluminum initial sol B, adjusting the pH value to 9-13, aging at the room temperature for 4-36h, and crystallizing at 130-180 DEG C for 40-120 h; and filtering the crystallization products, washing until the pH value filtrate reaching 7-9, drying the filter cake at 80-140 DEG C for 1-4 h, and calcining at 450-700 DEG C for 2-6 h. The molecular sieve has TON / MTT micro composite topology structure, and can be used for processing processes including isomerization-visbreaking, hydrocracking and catalytic cracking of petroleum fractions.