This paper proposes a probe-based force-controlled nanoindentation system employing a four-beam spring. The applied normal load is obtained by a force-modulation module with a four-beam spring and a capacitive displacement sensor, and the maximum normal force can be provided by this system is about 500 mN, which is determined by the precision approaching range of the probe in the vertical direction and the elastic yield strength of the four-beam spring. The closed-loop control accuracy of the normal force is about 0.3 mN. The penetration depth during the indentation process can be obtained by comparing the deflection of the four-beam spring with the elongation of the piezoelectric ceramic transducer (PZT). A rotating ring is utilized to control the orientation of the probe to broaden the machining diversity. The force-modulation module is set on a three-axes moving platform, and the relatively position between the probe and the sample surface can be controlled with a resolution of 1 nm in the horizontal plane, which indicates the high feeding accuracy between two adjacent indentations. Nanoindentation tests were performed using finite element (FE) simulation and experimental approaches with two typical indenters. In addition, 20 × 20 indentation arrays obtained by the probe rotation angles of 0° and 45° are also fabricated successfully. Based on these results, the feasibility of the developed system is verified for the probe-based force-controlled indentation-type micromachining.