A new approach for droplet coalescence in microfluidic channels based on selective surface energy alteration is demonstrated. The proposed method involves patterning the surface of cyclic olefin copolymer (COC), a hydrophobic substrate attached to a polydimethylsiloxane hydrophobic microchannel, with graphene oxide (GO) using standard microfabrication techniques. Surface wettability and adhesion analyses confirmed the enhancement of the COC surface energy upon GO patterning and the stability of the GO film on COC. Three representative cases are illustrated to demonstrate the effectiveness of the method on the coalescence of droplets for different droplet flow regimes, as well as the effect of changing the size of the patterned surface area on the fusion process. The method achieves droplet coalescence without the need for precise synchronization.