Abstract Take the flow characteristics of fluid in micro tube as the object, the characteristics of nonlinear filtration in low permeability reservoirs were studied using micro scale method by simulating the micro pore throat of reservoir with the micro tube which has the similar scale pore throat of low permeability reservoirs. The flow characteristics of de-ionized water flowing through fused silica capillary tubes with radius of 10.0 μm, 7.5 μm, 5.0 μm and 2.5 μm were investigated in experiments. Relationship between average flow rate and pressure gradient, effect of pressure gradient on fluid boundary layer, and relationships between flow resistance coefficient and Reynolds number were analyzed respectively in these experiments with different micro tubes. The flow of fluid through micro tubes with low velocity has nonlinearity, and the extent of nonlinearity increases with the tube radius decreasing. Nonlinear flow experimental points can be matched by quadratic curve. In micro flow, the percentage of effective fluid boundary layer thickness to micro tube radius decreases with the pressure gradient increasing. Research results indicated that Reynolds number can be used as the criteria of nonlinear flow. Flows with Reynolds number less than 10−3 have nonlinear features.