Based on single Cesium atoms trapped in a 1064 nm microscopic optical trap we have exhibited a single qubit encoded in the Cesium “clock states”. The single qubit initialization, detection and the fast state rotation with high efficiencies are demonstrated and this state manipulation is crucial for quantum information processing. The ground states Rabi flopping rate of 229.0±0.6 kHz is realized by a two-photon Raman process. A clock states dephasing time of 3.0±0.7 ms is measured, while an irreversible homogeneous dephasing time of 124±17 ms is achieved by using the spin-echo technique. This well-controlled single atom provides an ideal quantum qubit and quantum node for quantum information processing.