Exploration of deep mineralization, particularly where the mineralization of interest is covered by a conductive overburden, is still a challenge for the conventional transient electromagnetic (TEM) method, which measures TEM response using induction coils as the sensor. However, sensors such as fluxgate and superconductive quantum interfere device (SQUID) magnetometers can measure the B-field directly, which can provide more reliable deep information for mineralization exploration. In this paper, we report on the research and development of our newly developed high-temperature superconductor (HTS) SQUID magnetometer, which is cooled by liquid nitrogen at 77 K, and its application in TEM measurement for deep exploration in a gold deposit in China. This improved SQUID magnetometer version has a good performance with noise (60 fT/\(\sqrt {{\rm{Hz}}} \)), slew rate (0.8 mT/S), dynamic range (100 dB), sensitivity (6.25 mV/nT), and bandwidth (DC-20 kHz). To find deep and peripheral ore in the Baiyun gold deposit located in Liaoning Province, NE China, both the SQUID magnetometer and induction coil were used for TEM data acquisition. Results show that TEM can detect the distribution of local strata and the faults contained within them. Results also indicate that the SQUID magnetometer has superior response performance for response over geological targets with slower decay time when compared to the induction coil signals. The SQUID magnetometer is more sensitive at observing the induced-polarization effect which is closely related to the ore-controlling faults.