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The semi-airborne transient electromagnetic method adopts the working mode of ground transmitting and air receiving, which is very suitable for geological exploration in complex terrain areas. However, the topography and underground 3D anomalies have a serious impact on the semi-airborne transient electromagnetic response. The traditional 1D inversion or imaging technology based on layered model cannot meet the needs of fine interpretation of semi-airborne transient electromagnetic data. Therefore, based on the unstructured time-domain finite-element algorithm and the L-BFGS method, we developed a 3D inversion method for semi-airborne transient electromagnetic data. We apply our 3D inversion algorithm to the semi-airborne transient electromagnetic data interpretation of tunnel investigation and successfully determined the water-bearing area. The 3D inversion results can provide guidance for actual construction.