In order to solve the problem of poor inversion ability of multiple magnetic field sources inside small-scale objects, a multi-magnetic source inversion technology for small-scale objects was proposed. The atomic magnetometer was used to collect the magnetic source signal, the distribution of the magnetic source was inverted based on the theory of weak field, the distribution source model and Gauss-Seidel iterative algorithm were introduced to optimize the solution process, and the forward and inverse model was verified. At the same time, the point source model deconvolution operation was used to improve the spatial resolution of the magnetic source, and the spatial resolution of the system is about 10 mm before deconvolution and less than 4 mm after deconvolution. The results show that the spatial position distribution of the magnetic source inversion is roughly close to the real one, which verifies the correctness of the inversion technology and can be used for the identification of magnetic sources in precision instruments. This research has opened up a new way for the detection of multiple magnetic sources inside some precision instruments.