We propose a method which combines isogeometric analysis with the discontinuous Galerkin (DG) method for second and fourth order geometric flows to generate fairing surfaces, which are composed of multiple patches. This technique can be used to tackle a challenging problem in geometric modeling-gluing multi-patches together smoothly to create complex models. Non-uniform rational B-splines (NURBS), the most popular representations of geometric models developed in Computer Aided Design, are employed to describe the geometry and represent the numerical solution. Since NURBS basis functions over two different patches are independent, DG methods can be appropriately applied to glue the multiple patches together to obtain smooth solutions. We present semi-discrete DG schemes to solve the problem, and -stability is proved for the proposed schemes. Our method enjoys the following advantages. Firstly, the geometric flexibility of NURBS basis functions, especially the use of multiple patches, enable us to construct surface models with complex geometry and topology. Secondly, the constructed geometry is fair. Thirdly, since only the control points of the NURBS patches evolve in accordance with the geometric flows, and their number (degrees of freedom) is very small, our algorithm is very efficient. Finally, this method can be easily formulated and implemented. We apply the method in mean curvature flows and in quasi surface diffusion flows to solve various geometric modeling problems, such as minimal surface generation, surface blending and hole filling, etc. Examples are provided to illustrate the effectiveness of our method.