The invention discloses a digital spherical type three-axis magnetic flux gate magnetometer, which comprises a spherical three-axis magnetic flux gate sensor and a digital magnetic flux gate signal acquisition circuit. The spherical three-axis magnetic flux gate sensor is used for outputting analog voltage signals along the x axis, y-axis and z-axis directions. The digital magnetic flux gate signal acquisition circuit comprises an x-axis signal acquisition circuit, a y-axis signal acquisition circuit and a z-axis signal acquisition circuit, wherein the three signal acquisition circuits are the same in structure. The analog voltage signals along the x axis, y-axis and z-axis directions are input into the x-axis signal acquisition circuit, the y-axis signal acquisition circuit and the z-axis signal acquisition circuit, correspondingly. Each signal acquisition circuit comprises a first voltage follower, a signal attenuation module, a subtraction module, a second voltage follower, a low-pass filtering module, a programmable gain amplification module, an AD module, an MCU control module and a DA feedback module. According to the invention, the natural potential compensation technology, the automatic gain amplification technology and the AD conversion technology are adopted, so that the whole digital spherical three-axis magnetic flux gate magnetometer has the characteristics of low noise, high stability and high resolution.