Transmission laser bonding of dissimilar and biocompatible materials has a potential application in biomedical implants and their encapsulation processes. PET and glass are bonded together by employing micro-scale titanium on glass using a near infrared continuous wave (CW) diode laser. Radio frequency magnetron sputtering deposition method is used to prepare Ti coating on glass substrates. The effect of main process parameters including laser power, scanning speed and film thickness of Ti coating on bond strength and bond width is investigated through the experiments based on single process parameters. The effect of surface roughness of glass substrate on the roughness of Ti coating and the bond strength is discussed. The bond strength between Ti coating glass and PET is obtained by lap-shear test. The information of failure analysis of laser bonded specimens after mechanical lap-shear test are gathered by true colour confocal microscopy for materials. The information of chemical bond for Ti coated glass and PET is collected from laser transmission bonding process by using X-ray photoelectron spectroscopy (XPS). Experimental results show that the main process parameters including laser power, scanning speed have a significant impact on bond strenghth, and the bond strength increases with the thickness of Ti coating and the surface roughness of glass substrates. Based on this research, it will be helpful for transmission laser bonding between Ti coated glass and polymer.