In high power laser systems, the high-frequency noise generated by nonlinear effect is effectively removed by low-pass spatial filter, and the low-frequency noise passing through pinhole is always considered as very safe to optical devices in downstream. However, in practical applications both modulation contrast ratio and spatial frequency of the low-frequency noise will be changed and possibly become dangerous components, depending on different magnification ratios of spatial filter. In this paper, the evolution of low-frequency noise is theoretically analyzed and numerical simulated depending on different magnification ratios of spatial filter. The analysis results show that both modulation contrast ratio and spatial frequency of the low-frequency noise passing through pinhole will be changed 1/M times, where M is magnification ratio of spatial filter. For M<1, the safe low-frequency noise will be extruded into high-frequency which is the fastest growing components and finally develop into the most dangerous part to the damage of optical devices again. It is significant to consider the evolution of low-frequency noise in practical applications of spatial filter for high power laser system.