We present a new scheme for high-efficiency three-dimensional (3D) atom localization in a three-level atomic system via spontaneous emission. Owing to the space-dependent atom-field interaction, the position probability distribution of the atom can be directly determined by measuring the spontaneous emission. It is found that, by properly varying the parameters of the system, the probability of finding the atom at a particular position can be almost 100 %. Our scheme opens a promising way to achieve high-precision and high-efficiency 3D atom localization, which provides some potential applications to spatially selective single-qubit phase gate, entangling gates, and quantum error correction for quantum information processing.