Atomic force microscopy (AFM) probe vibration monitoring is essential for achieving accurate nanoscale imaging and reliable signal interpretation. This paper presents a low-noise vibration detection method based on a real-time FPGA-LabVIEW homebuilt system. The FPGA receives signals from a quadrant photodiode (QPD), performs analog-to-digital conversion and parallel processing, and integrates cascaded digital filters for noise reduction. A finite impulse response (FIR) low-pass filter extracts the static spot position, while an infinite impulse response (IIR) band-pass filter preserves the probe’s resonance vibrations. Compared with conventional analog detection, the proposed system reduces background noise by approximately 50% (measured as 50.23%), enhances the signal-to-noise ratio (SNR) from 15 dB to 20 dB, and maintains FPGA signal-processing latency below 5 μs. This work demonstrates that the proposed real-time FPGA-LabVIEW AFM noise optimization system significantly improves signal-to-noise ratio and real-time performance, providing a practical solution for high-precision, low-noise AFM imaging.