Clinical significance of anti-cancer effects of Huaier has been emphasized recently. We have proved that a broad spectrum of Huaier effects was based on the rescue of the disrupted Hippo signalling pathway, especially through the rescue of transcriptional dysregulation. We initiated clinical research for thorough understanding of mode of action by total RNA- and small non-coding RNA-sequencing. Here we provide the surprising genomic plasticity by Huaier observed in the time course of recovery from cancer. The extensive changes in RNA editing events were first observed, such as average 92,427 SNP variances per individual (22,688 in normal control). The subsequent changes in the process of translation and transcription resulted in the drastic changes in number of up/down-regulated transcripts. The ratio of the changes at maximum was 85% (23,210/27,447). With the advent of many novel sequences found in small nuclear RNAs and the consequent gene-silencing derived from miRNA-mediated post-transcriptional control, quantitative and qualitative changes of expression in transcriptional factors (mean 1,115/person) contributed to rescue dysregulated functions occurred in almost all required physiological functions for cancer recovery. The transcription control was demonstrated as functional lineage map between the core transcriptional factor and functionally linked transcripts, and the recovery could be clearly shown as the silencing of those massive changes in the end. The genetic alterations, especially related to the inhibition of NFκB and TGF-β signalling pathways showed significant effects on the improvement of prognosis. Thus, Huaier therapy contributes to cancer cell death with damaged tissue regeneration by extensive and systematic genomic modulations.