A sample replacement method base on the elastic force produced by the polydimethylsiloxane (PDMS) elastic membrane was established to reduce the fluid driving parts and sample consumption in the sample replacement. In the draining stage, the microvalve between sample reservoirs and cell culture pool was closed, the liquid in the cell culture pool was pumped out by using a micropump, and the elastic membrane at the top of the pool was collapsed. Once the elastic membrane was collapsed to a certain extent, the micropump and the microvalve between cell culture pool and sample waste reservoirs were closed, and the microvalve between cell culture pool and required sample reservoirs was opened immediately. The new sample would be taken into the pool by the elastic force generated from the elastic membrane bounce. The aforementioned steps were repeated several times and the sample wastes could be replaced. The main factors affecting the replacing effect, including the net pressure put on the top elastic membrane, the film thicknesses and the shape of the path from sample reservoirs to cell culture pool, were optimized according to the theoretical analysis, the finite element simulation and the experiment results. The optimal parameters are the film thickness to be 0.8 mm, the micropump flow rate 1.67 mL/min and the straight path, respectively. On the parameters mentioned above, more than 90% sample wastes are replaced within 80 s, meanwhile the sample consumption and fluid shear stress in the pool are less than 1/4 and 1/10 of the existing sample replacement system under the same replacing rate, respectively. The sample replacement method proposed shows its advantages on simple structure, low-sample/power consumption, and fewer-microchip mass, which is benefit to the miniaturization and automation of the space cell culture micro systems.