Carbon Nanotube (CNT) plays an important role in the field of nanotechnology because of their unique structural, mechanical properties and electrical properties. The density of CNT is very low which is about half of aluminium, and the strength of CNT is about 20 times stronger than steel, making them an excellent material with high natural frequencies. For this reason, nano carbon materials can be considered used as a non-contact atomic force microscope (NC-AFM) probe. In this study, the vibration analysis of Multi-Walled Carbon Nanotubes (MWCNT) is performed using the molecular dynamics (MD) method which is shown in Fig.1. We design a scanning probe by MWCNT including Single-Walled (SW) CNT, Double-Walled (DW) CNT, Triple-Walled (TW) CNT and Quadruple-Walled (QW) CNT with different lengths, as the shape of the probe in NC-AFM, and the specimen is graphene sheet (GS). The relationship between the change of natural frequency and the distance between the probe and specimen is discussed in detailed. The diameter of the innermost layer CNT in the analytical model is 3.892Å. The interlayer distance of the MWCNT is set to be the same r=3.114Å due to the van der Waals force between the adjoin layers. The results show that with the increasing of layers of MWCNT, the natural frequency becomes higher. Fig.2 shows that the natural frequency is increasing with shortening the distances between MWCNT and GS, while the distance is larger than 9Å the natural frequency becomes unchanging. Although the relationship between nature frequency and the distance is one-to-one, we can consider that the distance between NC-AFM probe and the specimen can be measured by the vibration frequency.