Ultrafast laser processing is a critical technology for micro- and nano-fabrication due to its ability to minimize heat-affected zones. The effects of intensity variation on the ultrafast laser ablation of fused silica were investigated to gain fundamental insights into the dynamic modulation of pulse intensity. This study revealed significant enhancement in ablation efficiency for downward ramp intensity modulation compared to the upward ramp. This effect was independent of the repetition rate ranging from 100 Hz to 1 MHz, which suggested that it originates from persistent residual effects of preceding pulses. Photoluminescence experiments indicated that the observed effect is primarily attributed to the dynamic reduction in the ablation threshold caused by the formation of defects such as non-bridging oxygen hole centers. The correlation between the sequence of intensity-modulated pulses and defect formation has been clarified. The knowledge of these correlations, combined with machine learning-based optimization methods, is useful for the optimization of the throughput and quality of ultrafast laser processing.