To improve the wettability of micro channels made of Polymethyl Methacrylate(PMMA) and Polydimethylsiloxane(PDMS), the wettability of PMMA and PDMS surfaces was modified through sputtering silicon dioxide. Firstly, the surfaces of PMMA and PDMS were etched with an oxygen plasma to change their surface morphologies and enhance the roughnesses. Then, a thin layer of silicon dioxide was sputtered on their surfaces for hydrophilic modification and the silicon dioxide layers with different thicknesses were obtained by different sputtering time. The contact angles of the PMMA and PDMS surfaces were measured within a period of time after the hydrophilic treatment, and the effects of hydrophilic modification under different conditions were evaluated. Finally the adhesivity of the modified samples was tested too. The experimental results show that the surface of PMMA after oxygen plasma etching remains extremely hydrophilcity during 10 days via 10 min dioxide sputtering, and the contact angle remains lower than 10° in 35 days with 15 min sputtering. The modified PDMS remains hydrophilcity and the contact angle lower than 60° for 10 days. The aging treatment delays the recovering of the hydrophobicity of PDMS. By silicon dioxide sputtering, the PMMA and PDMS after oxygen plasma etching achieves longer hydrophilic modification efficiency. Moreover, after hydrophilic modification, both modified PMMAs, or pristine PDMS and modified PDMS could be bonded effectively.