The scanning transmission X-ray microscopy (STXM) platform based on synchrotron radiation has achieved nanoscale imaging with chemical sensitivity using spectro-microscopy techniques. However, the quality of STXM imaging is affected by the stability of the beam intensity. The top-up operation mode of synchrotrons to maintain a constant electron beam intensity introduces periodic fluctuations in the X-ray beam intensity, leading to notable imaging noise that decreases both contrast and precision. To address this issue, a high-speed real-time beam intensity monitoring system was designed and implemented at the BL08U1A beamline of the Shanghai Synchrotron Radiation Facility. This system utilizes an yttrium-aluminium-garnet crystal along with dual detectors having an acquisition frequency of up to 1 MHz and a synchronization error of less than 20 ns between them. This system can precisely and synchronously monitor the X-ray beam intensity variations which are used to remove noise due to electron injection from STXM images, thereby markedly improving the quality of STXM imaging.