We investigate the isogeometric analysis for surface PDEs based on the extended Loop subdivision approach. The basis functions consisting of quartic box-splines corresponding to each subdivided control mesh are utilized to represent the geometry exactly, and construct the solution space for dependent variables as well, which is consistent with the concept of isogeometric analysis. The subdivision process is equivalent to the $h$-refinement of NURBS-based isogeometric analysis. The performance of the proposed method is evaluated by solving various surface PDEs, such as surface Laplace-Beltrami harmonic/biharmonic/triharmonic equations, which are defined on different limit surfaces of the extended Loop subdivision for different initial control meshes. Numerical experiments demonstrate that the proposed method has desirable performance in terms of the accuracy, convergence and computational cost for solving the above surface PDEs defined on both open and closed surfaces. The proposed approach is proved to be second-order accuracy in the sense of $L^2$-norm by theoretical and/or numerical results, which is also outperformed over the standard linear finite element by several numerical comparisons.