This paper presents new bonding and surface modification methods for plastic substrates utilizing atmospheric pressure plasma (AP plasma) treatment. Three kinds of AP plasma equipments including after-glow discharge, dielectric barrier discharge and flame type are tested and evaluated for their feasibility of microfluidic device fabrication. The experimental results show that the DBD plasma equipment is the most suitable one for microfluidic applications due to its low temperature and high treating level. Three kinds of polymenr including PMMA, PC and PDMS are used as the sample substrates for evaluating the performance of AP plasma in this study. Experimental results show that the polymer surface turns into hydrophilic after AP plasma treatment. Fourier Transform Infrared Spectroscopy (FTIR) inspection indicates that a new peak corresponding to -C-OH functional group is generated at the wavenumber of 1040 cm-1 after AP plasma treatment. X-ray photoelectron spectrum investigation also shows that the O/C (atom ratio) is 3.5-fold incensement in compare with the bare sample. SEM and AFM observations are utilized to evaluate the surface morphology change after plasma treatment. The measured surface roughness is at the level of several nanometers which is acceptable for most microfluidic applications. We develop two simple and high strength bonding methods for sealing microfluidic deivices in this study. The bonding process can be achieved in 6 minutes and bonding strength of 1.69 MPa and 3.81 MPa can be obtained using direct plasma bonding and ethyl alcohol assisted bonding, respectively. The bonding strength obtained using ethyl alcohol assisted bonding technique reported in this study is the highest one that ever been reported. The feasibility of AP plasma treatment for sealing microfluidic chips are confirmed by three examples including two novel passive microfluidic mixers and one cross-type micro CE chip. Experimental result shows that the mixing performance of the micromixer can reach up to 90% at an operation condition of a low Reynolds number of 4. In addition, micro CE chip sealed with the proposed method can successfully inject and separate dye sample with a long-term stability upto 30 minutes. Separation of 100 bp standard DNA sample of 100 bp to 3000 is also successfully demonstrated with high separation efficiency. It is the author¡¦s firm believes that the proposed bonding method will give substaintial impact on the fabrication of microfluidic device in the future.