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With the fast development of urban rail transportation, shield construction has been widely used in tunnel construction in China. It is very important to detect the random distribution of boulders, which may cause geological problems. Cross-hole electrical resistivity tomography (ERT) has the advantage of precise detection, but it has not been systematically studied in solitary rock detection. Therefore, we set up several numerical models and proposed weighted inversion, to improve the capacity for detecting boulders. Subsequently, the method was applied to the Xiamen Metro Line 1, where it was highly likely to encounter boulders. All the test boreholes revealed the presence of boulders, and their location and size were consistent with the geophysics results. This study demonstrated the suitability of weighted inversion based on a multi-configuration combination of cross-hole ERT for the detection of boulders. This case study provides new engineering perspectives on how to detect boulders.