Objective To review the clinical features and genetic test results of a case of Shwachman-Diamond syndrome caused by SBDS gene mutation but misdiagnosed as idiopathic short stature. Methods Clinical data, laboratory and imaging results and genetic data were collected and followed up. Results The patient was a boy aged 10 years and 11 months. Clinical manifestations included short stature, anemia and thrombocytopenia were indicated by laboratory examination, and the peak value of growth hormone stimulation test was 31 μg/L. Trio whole-exome sequencing revealed the presence of c.258+2T>C and c.286T>C complex heterozygous mutation, inherited from the proband's mother and father respectively; His younger brother also carried the same SBDS gene complex heterozygous mutations and exhibited similar clinical features, including short stature, anemia, thrombocytopenia, and leukopenia. Notably, the c.286T>C has not been previously reported in the literature and represents a novel mutation site. Growth hormone treatment for half a year, the height increased by 2.1cm, indicating poor therapeutic efficacy. Regular outpatient follow-up shows that there is still anemia and thrombocytopenia. Conclusion presenting with short stature complicated by bone marrow failure should be evaluated for Shwachman-Diamond syndrome, and genetic examination should be improved. The c.286T>C mutation identified in this case is a novel mutation site. In this instance, growth hormone therapy proved ineffective.