A light beam tightly focused by a high numerical-aperture lens system contains longitudinal components with polarization parallel to the propagation axis. By numerically analyzing the polarization distribution around the focal region in one pair of confocally aligned counter-propagating tightly focused light beams with orthogonal linear polarizations, we found that there exists a three-dimensional polarization gradient pattern similar to that used in cooling neutral atoms. This can be used to three-dimensionally cool atoms trapped in a far-off-resonant trap with only one pair of counter-propagating beams in one dimension. This new cooling scheme can be used to individually cool single atoms in an addressable two-dimensional single-atom array for quantum information processing and be applied to perform readouts of qubit encoded in these atoms without losing them.