Plagioclase, pyroxene and glass are the main component phases of different planetary materials. In situ Rb-Sr dating of these common phases thus would represent the timing of magmatic differentiation, effectively complementary to the rare, tiny U-Pb bearing phases that only form at a late stage. In this study, we selected lunar meteorites as examples to establish an in situ Rb-Sr dating method where plagioclase, pyroxene, ilmenite, and glasses were the laser-ablation (LA) targets. The accuracy of 87Sr/86Sr and 87Rb/86Sr measured by LA-MC-ICP-MS was better than 0.2 ‰ and 3 %, respectively, for samples with an 87Rb/86Sr ratio lower than 1. However, we found that the distributions of Rb and Sr in the natural materials were heterogeneous at the micrometer scale, leading to inaccurate 87Rb/86Sr ratio correction when calculated by normal data reduction methods. A new data reduction strategy of the smallest unit of isochron age (SUIA) was developed. Using the SUIA, the Rb-Sr isochron age of 2984 ± 43 Ma and 3149 ± 20 Ma was obtained for two lunar meteorites (NWA 10597 and NWA 6950, respectively). These results are identical within 1-2% deviation relative to the U-Pb dating ages for baddeleyite and apatite using SIMS. The present method may have broad applicability for determining the Rb-Sr isochron ages of other planetary samples.