We develop a decomposition method based on the augmented Lagrangian framework to solve a broad family of semidefinite programming problems possibly with nonlinear objective functions, nonsmooth regularization, and general linear equality/inequality constraints. In particular, the positive semidefinite variable along with a group of linear constraints can be decomposed into a variable on a smooth manifold. The nonsmooth regularization and other general linear constraints are handled by the augmented Lagrangian method. Therefore, each subproblem can be solved by a semismooth Newton method on a manifold. Theoretically, we show that the first and secondorder necessary optimality conditions for the factorized subproblem are also sufficient for the original subproblem under certain conditions. Convergence analysis is established for the Riemannian subproblem and the augmented Lagrangian method. Extensive numerical experiments on large-scale semidefinite programming such as max-cut, nearest correlation estimation, clustering, and sparse principal component analysis demonstrate the strength of our proposed method compared to other state-of-the-art methods.