We propose a new method for the development of multi-beam systems for the spatial alignment and stability of beams based on the error separation technique. This method avoids alignment errors caused by coupling effect of piezoelectric devices, inaccurate correction calculations, and detection mode of the angular deviation. According to the results by external detectors, the error value of spatial alignment and the root mean square (RMS) of deviations under control during 1 h can be equivalent to approximately 0.87 and 1.06 nm at the sample plane under an oil immersion lens (focal length f$=2\mathrm{mm}$). The RMS of deviations is less than one-third of those currently reported for multi-beam systems; therefore, higher alignment and stability accuracy can be achieved with our proposed method.