The increasing radio frequency interference (RFI) is a well-recognized problem in radio astronomy research. Pulsars and Fast Radio Bursts (FRBs) are high-priority science targets of the ongoing Commercial Radio Astronomy FAST Survey (CRAFTS). To improve the quality of RFI removal in searches of pulsars and FRBs based on CRAFTS multi-beam data, we here propose an intuitive but powerful RFI mitigation pipeline (CCF-ST). The “CCF-ST” is a spatial filter constructed by signal cross-correlation function (CCF) and Sum-Threshold (ST) algorithm. The RFI marking result is saved in a “mask” file, a binary format for RFI masks in PRESTO. Three known pulsars, PSR B0525-21, PSR B0621-04, and PSR J0943 + 2252 from CRAFTS L-band 19 beams data are used for evaluation of the performance of CCF-ST in comparison with other methods, such as PRESTO’s “rfifind”, ArPLS-ST and ArPLS-SF. The result shows that CCF-ST can reduce effective data loss rate and improves the detected signal-to-noise ratio of the pulsations by ∼26% and ∼18% respectively compared with PRESTO’s “rfifind” and ArPLS-ST. The CCF-ST also has the advantage of low computational cost, e.g., reducing the time consumption by ∼40% and memory consumption by ∼90% compared with ArPLS-SF. We expect that the new RFI mitigation and analysis toolkit (CCF-ST) demonstrated in this paper can be applied to CRAFTS and other multi-beam telescope observations to improve the data quality and efficiency of pulsar and FRB searches.