Membrane proteins are generally of natural low abundance and insoluble to aqueous solutions. Thus, investigation of membrane proteins is relatively hampered since efficient separation of membrane proteins are rather challenging. Microseparation approaches certainly play an essential role in fulfilling such demanding investigations due to their significant advantages of high throughput, reduced separation time, and low sample consumption. In this review, recent developments of microseparation are documented with aspects of three key separation methods, including CE, micro-LC and microchip. Preparation of membrane proteins prior to separation is also discussed, including solubilization and preconcentration. Certainly, more applications of microseparation approaches in membrane protein separations can be expected in the near future.