The micro-orifices during the Joule-Thomson process are used in a variety of energy applications such as microfluidic systems and large-scale cryogenic helium systems. The structure of the micro-orifice impacts the cooling capacity by adapting the mass flow rate and pressure drop in the refrigeration system. The pressure drops and flow characteristics in micro-orifices with diameters of 20–40 μm and thicknesses of 50 μm were numerically and experimentally investigated. Helium was used as the working fluid, and the simulations using CFD (Computational Fluid Dynamics) method were conducted with upstream pressure (pu) of 0.5–2.0 MPa (Mega-Pascal) and downstream pressure (pd) of 0.1–1.5 MPa at 293 K (Kelvin). The simulations found that the completely choked pressure ratio of each micro-orifice is smaller than the theoretical critical pressure ratio λ*=0.487 and revealed the flow field characteristics in micro-orifices flow under different working conditions. Experiments were carried out with four micro-orifices with the thickness of 50 μm and the effective diameter of 23.88 μm, 26.53 μm, 33.30 μm, 40.69 μm under different pressure conditions (pu 0.5–2.0 MPa, pd 0.1–1.5 MPa), respectively. The errors between the numerical and experimental mass flow rates in different micro-orifices corresponding to the pressures are within 10 %. The W. B. Brower model was used to predict the mass flow rates that are consistent with the experiments and simulations. The semi-empirical model is developed using the data set for the modifications to W. B. Brower model and with an error range of ± 0.08 mg/s in the calculated flow rate compared to the experimental value.