The invention discloses a method for preparing a magnetic 5A molecular sieve from coal gangue and application of the magnetic 5A molecular sieve. The method comprises the following steps: after milling coal gangue, performing high-temperature roasting by using sodium carbonate to activate the coal gangue; performing oxidization at low temperature, adding hydrochloric acid, performing soaking at 90DEG C, performing filtration, and adding sodium hydroxide and cobalt acetate into the filtrate to prepare iron cobaltate; after washing the solid, performing drying, adding a sodium hydroxide solid,performing uniform mixing by grinding, and performing low-temperature alkali fusion; and adding deionized water, calcium chloride and citric acid, performing aging at 60 DEG C, adding the iron cobaltate, and performing ultrasonic treatment to synthesize the magnetic 5A molecular sieve by crystallization. The 5A molecular sieve prepared by the method has the advantages of favorable oxidation resistance, high specific surface area, high adsorbability and the like, and the product can be easily subjected to solid-liquid separation through an external magnetic field; and the 5A molecular sieve solves the problem of high synthesis cost of the molecular sieve, provides a new way for cyclic, refined and efficient utilization of coal gangue, achieves the effect of changing wastes into valuable substances, and satisfies the requirements of environmental protection and low carbon.