We report the result of a non‐destructive elemental analysis of lunar meteorites using a negative muon beam at J‐PARC. An experimental system of six Ge semiconductor detectors and a newly designed He analysis chamber (to enable quantitative analysis of Al) was used to provide a high signal‐to‐noise ratio for the detection of major elements from lunar rocks (Mg, Si, Fe, O, Ca, and Al). We performed a Monte Carlo simulation to determine the chemical compositions at two sides and the center of a sample (at depths of 0.33 and 0.96 mm below the sample surface, respectively) of the lunar meteorite DEW 12007. These results indicate that the three interior regions of DEW 12007 are likely to be 55.8:44.2, 51.4:48.6, and 54.4:45.6 wt% mixtures of anorthositic and basaltic clasts, respectively. This study is the first quantitative analysis of a heterogeneous meteorite interior using a negative muon beam. As elemental analysis using a muon beam is non‐destructive and highly sensitive to light elements, including C, N, and O, the protocols established in this study are applicable to initial characterization of returned samples from the South Pole of the Moon.