The present invention relates to a substrate surface treatment method for substrate bonding, comprising the steps of (a) oxidizing a substrate surface formed of thermoplastic and then introducing an amino group into the substrate surface; and (b) reacting an epoxy modified silicone material with the substrate surface to form a coating layer, and to a substrate bonding method comprising the substrate surface treatment method. According to the present invention, a low-molecular weight PDMS coating layer is formed on a surface of the thermoplastic substrate by forming an amine-epoxy bond under room temperature and atmospheric pressure conditions, thereby a thermoplastic-PDMS substrates bonded body or thermoplastic-thermoplastic substrates bonded body having strong and reproducible irreversible bonding regardless of the kind of thermoplastic. In particular, a microfluidic apparatus is manufactured using the substrate bonding method according to the present invention, thereby preserving the distinctive light transmittance of the plastic substrate itself without affecting the shape and profile of the microchannel formed before substrate bonding, and realizing high pressure resistance through strong bonding, and thus the present invention can be useful for downsizing a high-throughput pre-treatment apparatus capable of processing a great deal of samples and constructing a portable platform.COPYRIGHT KIPO 2015