We have studied five intersecting integrated geophysical profiles for the 3D crustal structure of the Lu (Lujiang)-Zong (Zongyang) ore district to obtain a better understanding of the metallogenesis and provide in-depth information for deep mineral targeting. The profiles, totaling more than 300 km, have reflection seismics and magnetotelluric sounding. Regional gravity surveys were also integrated into this study. New discoveries were obtained regarding the upper crustal structure and deformation based on the integrated analysis of these data. The Lu-Zong ore district consists of four major crustal blocks. They are the Shaxi uplift, Qianshan-Kongcheng Depression (QKD) in the west, Lu-Zong volcanic basin, and the Along-River uplift in the east. The north–south crustal elements show the northward “step-type” uplift, juxtaposed by two steplike faults, the west–northwest/east–southeast-trending Tangjiayuan-Zhuanqiao Fault and the Lujiang-Huangguzha-Tongling Detachment (LHTD) Fault. The Lu-Zong volcanic basin presents a nonsymmetrical shape with four inward-dipping boundary faults. The northern and eastern boundary faults (BF2 and LHTD) are deep faults, which control the development and evolution of the Lu-Zong volcanic basin. There are three west–northwest/east–southeast-trending faults and six northeast–southwest-trending faults cutting over the ore district. From north to south, they are the LHTD Fault, Tangjiayuan-Zhuanqiao Fault, and Yijing-Taojiaxiang Fault (BF3); from west to east, the six faults are the Tan-Lu, Chuhe, Luohe-Quekou, Zongyang-Huangtun, Taojiawan-Shijiawan, and Changjiang Thrust Fault (CTF). The formation and evolution of the ore-district are mainly affected by the Yanshanian intracontinental orogeny, and they experience the Middle to Late Jurassic compression and subsequent Cretaceous extension, possibly due to the paleo-Pacific northwest-trending subduction. Our studies determined that the CTF is a thrust system in nature and the LHTD is a southwest-dipping detachment. Two Jurassic basins were found, surrounding the northeast and southeast of Lu-Zong volcanics, which may be due to the product of postcollision extension of Indosinian orogeny during the middle and early Late Triassic.