The invention provides an intermediate layer magnetic field remote sensing device based on gated photon counting, and relates to the field of intermediate layer magnetic field laser remote sensing. The device comprises a continuous wave laser (1), an acoustic-optical modulation unit (2), an emission telescope (3), a reception telescope (4), a detection unit (5), an FPGA gated photon counting unit(6) and a computer (7). A pulse signal modulated by laser intensity is generated by employing an FPGA, and the function of gated photon counting is realized. Gated time delay is adjusted, resonance fluorescence emitted by a neutral atom layer of an intermediate layer is received, the repetition frequency of a pulse is scanned, and a magnetic resonance signal is obtained. The magnetic field of theintermediate layer is remotely detected to provide a new tool for drawing of a magnetic field structure of an earth lithosphere and long-term monitoring of the ionosphere current of a polar region. The intermediate layer magnetic field measuring scheme based on gated photon counting can only receive echo waves from the neutral atom layer at the specific height, and the measurement of the magneticfield of the intermediate layer with distinguishable height can be realized.