In the pursuit of modern microfluidic chips with multifunction integration, micronanofabrication techniques play an increasingly important role. Despite the fact that conventional fabrication approaches such as lithography, imprinting and soft lithography have been widely used for the preparation of microfluidic chips, it is still challenging to achieve complex microfluidic chips with multifunction integration. Therefore, novel micronanofabrication approaches that could be used to achieve this end are highly desired. As a powerful 3D processing tool, femtosecond laser fabrication shows great potential to endow general microfluidic chips with multifunctional units. In this review, we briefly introduce the fundamental principles of femtosecond laser micronanofabrication. With the help of laser techniques, both the preparation and functionalization of advanced microfluidic chips are summarized. Finally, the current challenges and future perspective of this dynamic field are discussed based on our own opinion.