A novel six-probe measurement system is proposed for reconstructing deep hole axes. This system is based on the two-point method in three dimensions. The probe can obtain the center position of the measured section and radius of the circle at each step. This novel approach has the following advantages. 1) The effects of the straightness error of the sensor motion device on the axis measurement and fitting results can be eliminated. 2) The approach has remarkable universality. The holes with different apertures can be measured by adjusting the relative position between displacement sensors. 3) Probe movement and data acquisition can be realized automatically which reduces the amount of labor and improves measurement efficiency. 4) The process of measurement is simple; the hole axis can be fitted using only a single scanning measurement, after which related parameters can be evaluated. These advantages were demonstrated by theoretical analyses and simulations. Further, experiments showed that this novel system can provide high lateral resolution.