Atomic force microscope (AFM) is a powerful instrument for nanoscale measurement in different environments. Since high-resolution AFM measurements require avoiding external vibration interference, bulky vibration isolation platforms are commonly applied, which is a limitation for in-situ AFM measurements in some environments with small space and limited loads. For high-resolution imaging without bulky external vibration isolation, this paper presents a vibration isolation method for AFM with its internal z-axis (vertical) actuators moving the AFM probe. A piezoelectric actuator was used for z-axis actuation, and a flexural structure with low stiffness was designed to guide the z-axis motion and achieve vibration isolation. The low stiffness mechanically isolated the probe from floor vibrations at high frequencies. The parameters of the flexural structure were determined theoretically, and its performance was analyzed through finite element method. Finally, the prototype of the platform was machined and its vibration isolation performance was experimentally tested. The experimental results indicate that the vibrational isolation effect of the designed flexural structure is increased by 51 % in the z-axis in the frequency range 0.1–300 Hz and above 900 Hz compared to the original AFM structure.