The invention provides a multi-rotor unmanned aerial vehicle helium optical pump aeromagnetic measurement system. The multi-rotor unmanned aerial vehicle helium optical pump aeromagnetic measurement system comprises carbon fiber propellers, brushless motors with magnetic shielding functions, carbon fiber arms, a carbon fiber frame, an external cover, a magnetic probe rod, a battery, a digitized helium optical pump magnetometer host, a magnetic probe collection and release system, a flight control data transmission module, a long-distance Bluetooth communication module, a GPS antenna, a helium optical pump probe, a magnetic compensation coil, a magnetometer monitoring panel and a flight control panel. The multi-rotor unmanned aerial vehicle helium optical pump aeromagnetic measurement system has low requirements for take-off and landing sites, can carry out hovering fixed-point magnetic field measurement and has a hardware magnetic compensation function; the magnetic probe has a collection and release function; the arms can be folded so as to transferred; and the multi-rotor unmanned aerial vehicle helium optical pump aeromagnetic measurement system is very suitable for small-areas aeromagnetic measurement conditions such as archaeology, river pipeline detection and non-explosive search.