We demonstrate a coherent microwave manipulation of a single optical photon based on a single Rydberg excitation in an atomic ensemble. Due to the strong nonlinearities in a Rydberg blockade region, a single photon can be stored in the formation of Rydberg polariton using electromagnetically induced transparency (EIT). The manipulation of the stored single photon is performed by applying a microwave field that resonantly couples the nS1/2 and nP3/2, while the coherent readout is performed by mapping the excitation into a single photon. We achieve a single photon source with g(2)(0) = 0.29 ± 0.08 at 80S1/2 without applying microwave fields. By implementing the microwave field during the storage time and retrieval process, we show the Rabi oscillation and modulation of stored photons that can be controlled to retrieve early or late. Rapid modulation frequencies up to 50 MHz can be obtained. Our experimental observations can be well explained via numerical simulations based on an improved superatom model accounting for the dipole-dipole interactions in a Rydberg EIT medium. Our work provides a way to manipulate the stored photons by employing the microwave field, which is significant for developing quantum technologies.