The objective of this paper is twofold. First, we conduct a careful study of various functional inequalities involving the fractional Laplacian operators, including nonlocal Sobolev-Poincare ', Nash, Super Poincare ' and logarithmic Sobolev type inequalities, on complete Riemannian manifolds satisfying some mild geometric assumptions. Second, based on the derived nonlocal functional inequalities, we analyze the asymptotic behavior of the solution to the fractional porous medium equation, partial derivative(t)u+(-Delta)(sigma) (|u|(m-1)u) = 0 with m > 0 and sigma is an element of (0, 1). In addition, we establish the global well-posedness of the equation on an arbitrary complete Riemannian manifold.