Spray freeze drying is an attractive technology for fabricating pharmaceutical powder, but it is still challenging to tailor the microparticle physical and chemical structure. Herein, a series of uniform mannitol microparticles with controllable morphology and crystal properties were successfully fabricated via a self-developed micro-fluidic jet spray freeze tower. The effects of feed solution composition and freezing temperature on microparticle size, morphology, surface architecture and crystal property were investigated to propose the particle formation mechanism. Freezing temperature showed more apparent effect on the microparticle characteristics with higher solid content (10 and 15 w/w%) in aqueous solution; Whereas the addition of ethanol as a co-solvent had a notable impact on microparticle morphology, concurrently perturbing the crystallization tendencies of mannitol. These results provide new insights for producing spray freeze dried pharmaceutical microparticles.