Mixture of gas molecules must be accurately detected for gas sensor. However, there are certain difficulties in identifying the type of gas and detecting its concentration by chemical sensors. SERS (Surface Enhanced Raman Scattering) is a promising method for high sensitive gas detection because of its ability of molecule discrimination. However, it is difficult for SERS sensor to identify gases with the similar structure. In this research, we have developed a more selective SERS sensor with molecular filter layers. Molecular filter property is studied by coating a filter polymer film on the SERS substrate. The characteristics of the sensor with two membrane structures were also studied and different filtering properties were obtained.