Background: Compared with the first-generation tyrosine kinase inhibitor (TKI), Nilotinib exhibited potent inhibition for BCR-ABL kinase activity, approved of the first-line and second-line TKI treatment of CML patients. Nilotinib was generally well tolerated with mild hematologic and non-hematologic adverse events. Hyperbilirubinemia, the most common non-hematologic adverse events, was confirmed presented mostly with grade I-II, rarely with grade III-IV in several large-scale clinical trails and real-world treatment. Case presentation: we report a rare case of elderly CML with severe bilirubin and creatinine elevation after receiving Nilotinib as second-line treatment for 2 years. After TKI suspension, hepatic and renal function improved quickly, but degree IV bone marrow suppression persisted for rather a long time. Monosomy 7 clone was detected at the point when renal dysfunction occurred, which indicated disease progression to accelerated phase. When Imatinib and Dasatinib were administrated alternately, a large area of acute cerebral infarction occurred unexpectedly after blood cell count recovered. So far, Imatinib treatment was continued, the patient is still stable state at the 6 months follow up.Conclusions: The report alerted clinicians to obsereve the incidence of adverse events during long-term TKIs therapy. Also, clinicans might consider the occurrence of monosomy clone when faced with poor efficacy or intolerance.