Abstract The prospects for expanding the mineral resource base in many countries are linked with the exploration of stranded sites localized at unexplored areas with complex natural and landscape conditions that make any ground survey, including magnetic prospecting, difficult and expensive. The current level of geology requires high-precision and large-scale data at the first stages of geological exploration. Since 2012, technologies of aeromagnetic surveying with unmanned aircraft vehicles (UAV) enter the market, but most of them are based on big fixed-wing UAV and do not allow to substantially increase the level of survey granularity compared with traditional aerial methods. To increase the scale of survey, it is necessary to reduce the altitude and speed of flight, for which the authors develop the methodical and technical solutions described in this article. To obtain data at altitudes of 5 m above the terrain even in a rugged relief, we created heavy multirotor UAVs that are stable in flight and may be used in a wide range of environmental conditions (even a moderate snowfall), and develop a special software to generate flight missions on the basis of digital elevation models. A UAV has special design to reduce magnetic interference of the flight platform; the magnetic sensor is hung below the aircraft. This technology was conducted in a considerable amount of magnetic surveys in the mountainous regions of East Siberia between 2014 and 2016. The results of the comparison between airborne and ground surveys are presented, which show that the sensitivity of the developed system in conjunction with low-altitude measurements can cover any geologically significant anomalies of the magnetic field. An unmanned survey is cheaper and more productive; the multirotor-based technologies may largely replace traditional ground magnetic exploration in scales of 1:10,000−1:1000.