A femtosecond fiber laser is extensively used in the field of precision micro-hole manufacturing because of its short pulse width, high instantaneous power, and nonselectivity for processing materials. This study proposes a high-precision trajectory adjustable beam scanning system, which uses a motor to control the angle of the deflection wedge group and the parallel plate group relative to the laser optical axis. Then, it narrows the spot through a focusing lens to achieve precise control of femtosecond laser rotation scanning. Moreover, it solves the current problems of high depth-to-diameter ratio and difficult inverted taper hole machining. The system is applied for processing the oil hole of the automobile fuel injector, and the aperture of the processing aperture is 25—800 μm, and the aperture error is ≤±2 μm. A micro-hole taper can be achieved at -5°—+5° in taper hole processing. Micro-hole machining with a depth-to-diameter ratio of 20∶1 is achieved.