Coronavirus disease 2019 (COVID-19) can affect the haematopoietic system. Thrombocytopenia at admission was prevalent, while late-phase or delayed-phase thrombocytopenia (occurred 14 days after symptom onset) is rare. This retrospective, single-centre study screened 450 COVID-19 patients and enrolled 271 patients at the Union Hospital, Wuhan, China, from January 25 to March 9, 2020. COVID-19-associated delayed-phase thrombocytopenia occurred in 11.8% of enrolling patients. The delayed-phase thrombocytopenia in COVID-19 is prone to develop in elderly patients or patients with low lymphocyte count on admission. The delayed-phase thrombocytopenia is significantly associated with increased length of hospital stay and higher mortality rate. Delayed-phase nadir platelet counts demonstrated a significantly negative correlation with B cell percentages. We also provided and described bone marrow aspiration pathology of three patients with delayed-phase thrombocytopenia, showing impaired maturation of megakaryocytes. We speculated that immune-mediated platelet destruction might account for the delayed-phase thrombocytopenia in a group of patients. In addition, clinicians need to pay attention to the delayed-phase thrombocytopenia especially at 3-4 weeks after symptom onset.