In this paper, dynamics of a suspended microchannel resonator (SMR) will be derived using the strain gradient theory. Accordingly, the size dependent governing equation and corresponding boundary conditions will be obtained using the extended Hamilton’s principle for open systems. The proposed strain gradient theory has three length scale parameters which can be reduced to the modified couple stress theory and the classical theory when two of three length scale parameters or all of them are set to zero, respectively. Also, the size effect of micro-flow associated with the flow velocity profile will be considered in the governing equation of motion. The stability analysis is then carried out to obtain complex frequencies and critical flutter speeds. Finally, the effects of flowing particle in the microchannel and the associated frequency shifts induced by the added mass will be studied.