The recent theoretical prediction and experimental realization of topological insulators (TI) has generated intense interest in this new state of quantum matter. The surface states of a three-dimensional (3D) TI such as Bi_2Te_3, Bi_2Se_3 and Sb_2Te_3 consist of a single massless Dirac cones. Crossing of the two surface state branches with opposite spins in the materials is fully protected by the time reversal (TR) symmetry at the Dirac points, which cannot be destroyed by any TR invariant perturbation. Recent advances in thin-film growth have permitted this unique two-dimensional electron system (2DES) to be probed by scanning tunneling microscopy (STM) and spectroscopy (STS). The intriguing TR symmetry protected topological states were revealed in STM experiments where the backscattering induced by non-magnetic impurities was forbidden. Here we report the Landau quantization of the topological surface states in Bi_2Se_3 in magnetic field by using STM/STS. The direct observation of the discrete Landau levels (LLs) strongly supports the 2D nature of the topological states and gives direct proof of the nondegenerate structure of LLs in TI. We demonstrate the linear dispersion of the massless Dirac fermions by the square-root dependence of LLs on magnetic field. The formation of LLs implies the high mobility of the 2DES, which has been predicted to lead to topological magneto-electric effect of the TI.