The invention discloses a silicon-aluminum-phosphate molecular sieve and a synthesis method thereof. The molecular sieve comprises elements of phosphorus, silicon, aluminum and oxygen and has the microtopography of a pyramid. The synthesis method comprises steps of mixing a silicon source, a phosphorus source, an aluminum source, water and a template agent, stirring, crystallization, washing, drying, roasting and the like. Due to the microtopography of the pyramid, molecules can be diffused within a relatively short distance inside molecular sieve channels at a relatively rapid diffusion velocity, pores in the surface of the molecular sieve are difficult to block, the selectivity of the molecular sieve is improved by 5%, and the service life of the catalyst is prolonged by one time.