The study on the effect of micro-nanostructures on the slip length of fluid boundaries in microchannels plays a crucial role in the field of microfluidics. In microfluidics, there exists a close relationship between surface micro-nanostructures and boundary slip effects. The work aims to delve into the impact of micro-nanostructures with different parameters on the slip length of fluids in microchannels, providing a deeper understanding of flow behavior in microfluids. By utilizing the finite element method and simulation software, microchannel models with three different microstructure shapes (square, cylindrical, and triangular prisms) in Cassie state are established. Physical fields are selected, fluid material properties are defined, boundary conditions are set, meshes are generated, and geometric parameters are adjusted for each model with different micro-nanostructure shapes, sizes, and spacing. Integral calculation of channel flow rate is conducted by defining a two-dimensional cross-sectional area at the channel outlet. The variation in channel flow rate is then utilized to assess the magnitude of the slip length. Based on the basic condition of Navier slip, the relationship between pressure drop, volume flow rate, and slip length of two infinite parallel plates is determined to derive a theoretical model for slip length calculation. The simulated results and relevant parameters are incorporated into the model to ultimately obtain the slip length of fluid flow on channel surfaces with different micro-nanostructures.