In the present study, a homemade probe-based nanometric morphology measurement system is proposed, which can be easily integrated with other probes, such as a diamond probe and an electrochemical electrode. In this system, an intermittent-contact mode is adopted, which is based on a set of micro-force servo modules. The micro-force serve module is mainly composed of a piezoelectric ceramic transducer, a capacitive displacement sensor, an excitation piezoelectric ceramic ring, and a four-beam spring. The four-beam spring integrated with a diamond probe is driven by the excitation piezoelectric ceramic ring. The mechanical structure and the control system of the measurement system are also designed. The vibration amplitude and the resolution of a normal load are calibrated during the engagement process under open-loop control. Moreover, the optimal values for parameters P, I, and D are obtained for the closed-loop measurement. The performance of the developed system is verified by measuring a standard sample. The measured depths agree well with the results obtained by commercial atomic force microscopy. The developed system can be used to measure nanostructures with high precision.