Hydrogel structures equipped with internal microchannels offer more in vivo-relevant models for construction of tissues and organs in vitro. However, currently used methods of constructing microfluidic devices are not suitable for the handling of hydrogel. This study presents a novel method of fabricating hydrogel-based microfluidic chips by combining casting and bonding of hydrogel sheets. Commonly, it is difficult to bond the hydrogel sheets together due to the hydro-interface. Here, a twice cross-linking strategy is designed to obtain a bonding interface that has the same strength with the hydrogel bulk. This strategy could be applied to arbitrary combinations of biocompatible hydrogels. Among the alternative composite hydrogels, the combination of gelatin and GelMA has shown the best biocompatibility and could promote the cell functionalization. Microscopic images and mechanical testing results demonstrate that the microfluidic channels are complete and stable while the hydrogel sheets are bonded together successfully. It is convenient to achieve the construction of hydrogel structures with channels in various forms. As an application, endothelial cells (ECs) are cultivated on the microchannel surface to construct a vessel model. The successful formation of functional endothelial monolayer within the fabricated channel is confirmed, indicating that the proposed method could produce interconnected predefined microfluidic networks within hydrogel to facilitate the spreading of ECs. Taken together, a facile and cytocompatible approach is developed for engineering a user-defined hydrogel-based chip that could be potentially useful in developing vascularized tissue or organ models.