A method of molecular sieve alkali metal ion exchange comprises the following steps: mixing and contacting an alkali metal molecular sieve, deionized water and magnetic hydrogen cation exchange resin, separating at least part of magnetic hydrogen cation exchange resin with hydrogen ions substituted by alkali metal ions from the slurry obtained after mixing and contacting by the magnetic field. The molecular sieve obtained by the method of molecular sieve alkali metal ion exchange provided by the invention has a low Na2O content; the molecular sieve performance requirements can be completely met after exchange once or for many times; more importantly, the method of the invention does not generate ammonium-containing waste water, is environment friendly; in addition, the method of the invention can omit one or two high temperature roasting processes in the prior art, and can reduce the energy consumption during the molecular sieve production process.