We reveal a novel topological property of the exceptional points in a two-level parity-time symmetric system and then propose a scheme to detect the topological exceptional points in the system, which is embedded in a larger Hilbert space constructed by a four-level cold atomic system. We show that a tunable parameter in the presented system for simulating the non-Hermitian Hamiltonian can be tuned to sweep the eigenstates through the exceptional points in parameter space. The non-trivial Berry phases of the eigenstates obtained in this loop from the exceptional points can be measured by the atomic interferometry. Since the proposed operations and detection are experimentally feasible, our scheme may pave a promising way to explore the novel properties of non-Hermitian systems.