The invention relates to a longitudinal magnetic field modulation based three-axis vector atom magnetometer and use method thereof and belongs to the technical field of low-intensity magnetic field detection. The longitudinal magnetic field modulation based three-axis vector atom magnetometer comprises a pumping optical path composed of a No.1 895nm DFB semiconductor laser, a No.1 convex lens, a No.2 convex lens, a No. 1 linear polarizing film and a Gamma/4 slide; a detection optical path composed of a No.2 895nm DFB semiconductor laser, a No.3 convex lens, a No.4 convex lens, a No. 2 linear polarizing film, a Wollaston prism and a balance detector; a three-dimensional magnetic field generating device composed of a No.1 Helmholtz coils, a No.2 Helmholtz coils and a No.3 Helmholtz coils in mutual orthogonality; a heating device; an atomic gas cell; a locking amplifier; and a signal processing system. According to the invention, since longitudinal magnetic field modulation is adopted, technical noise can be reduced in a comparatively large degree. Therefore, extremely high flexibility is achieved. Besides, by utilizing longitudinal magnetic field modulation, inter-axis crosstalk can be reduced, so that magnetic field direction detection becomes more accurate.