Depth‐profiling measurements of both the abundances of rare earth elements (REEs) and U‐Pb ages from zircons were conducted using a time‐of‐flight based inductively coupled plasma‐mass spectrometer (ICP‐ToF‐MS) coupled with laser ablation sampling. To improve ion transmission, a dry plasma cone from Nu Instruments was applied to the ICP‐ToF‐MS system employed. The signal‐to‐noise ratios for the analytes were further improved using a multiple spot‐laser ablation (msLA) protocol. Moreover, constructing a ‘moat’ around an analysis area obviated the risk of mixing of particles released from different layers. With the technique developed here, reproducible analyses of REE abundances and U‐Pb ages for three reference material zircons (91500, Plešovice and OD‐3) were performed for sampling depths in the range 0.59–0.66 μm. The present technique was also applied to zircon samples collected from the Himalayan orogen. The combination of REE abundances and U‐Pb isotopic ratios suggested that the discordant trend in U‐Pb isotopic ratios observed in this study was mainly due to mixing among three components in grains (thin outer layer, inner rim and core). The geochemical data obtained demonstrate that the combination of the msLA technique and ICP‐ToF‐MS system is a powerful tool to decode the multiple thermal events contributing to sample formation.