Nonmuscle myosin heavy chain 9 related diseases (MYH9-RD) are part of the causes of hereditary thrombocytopenia, and are often accompanied by renal injury, sensorineural deafness, cataract and other manifestations other than blood system. The patient was a 13-year-old girl with thrombocytopenia for more than 12 years and hematuria and proteinuria for more than 4 years. Peripheral blood smear microscopy showed a decrease in platelet count [(10-30)×10⁹/L] and an increase in platelet volume. Urine routine examination showed protein (+++) and erythrocyte (15-17/HP). The 24-hour urine protein quantification was 4.34 g [equivalent to 76 mg/(kg·d)]. Pure tone threshold measurement suggested high-frequency hearing impairment, and ophthalmic examination showed early-onset cataract. Genetic testing confirmed that the child had a heterozygous variation at c.2104c > t (p.r702c) of MYH9 gene, which was a reported pathogenic variation. Pedigree verification indicated that both parents and elder brother were wild type. MYH9-RD was subsequently diagnosed. Although the child was treated with valsartan and cyclosporine successively, renal damage continued to progress and entered to CKD2 stage. Cataract and hearing impairment were also worsened. For children with refractory thrombocytopenia, it is necessary to be alerted to the possibility of MYH9-RD, and genetic testing is helpful for early diagnosis.