Directly controlling the clustering process in transparent solids is an effective way to tune the properties of clusters and is important for integrated devices. Herein, single‐pulse ultrafast laser (UFL) micromachining is conducted as a facile technique to engineer the ultrafast clustering of metal in glass. Stable Ag clusters with few atoms are generated without thermal activation and exhibit efficient emission. Consequently, the clustering efficiency is enhanced by more than a thousand times compared with that of previous studies. The photoluminescence (PL) intensity and diameter of the emissive dots are precisely tailored by adjusting the number of pulses, pulse energy, and Ag doping concentration. It is confirmed that single‐pulse UFL micromachining is significantly superior in creating submicrometer luminescent structures compared with multipulse writing. High‐capacity optical information storage with a high signal‐to‐noise ratio is demonstrated by directly writing Ag clusters in 3D. Single‐pulse UFL micromachining enables precise fine tuning of the local chemistry of transparent solids and opens perspectives for the construction of functional micro/nanostructures and devices in 3D with a high throughput.