We analyze the decoherence between two ground electronic states of an optically trapped atom by adopting a full description of the atomic wavefunction. The motional state, i.e., the phonon state, is taken into account. In addition to the decoherence due to the variance of differential light shift (DLS), a new decoherence mechanism, phonon-jumping-induced decoherence (PJID), is discovered and verified experimentally. A coherence time of $T_2\approx 20$ s is then obtained for a single Cs atom by suppressing both variances of DLS and PJID by trapping the atom in a blue-detuned BBT and preparing the atom into its three-dimensional motional ground states. Our work opens a new prospect to extend the coherence time of optically trapped single atoms.