Abstract: Objective To explore the trends of anxiety and depression in patients during hematopoietic stem cell transplantation (HSCT) and analyze their influencing factors. Methods A total of 82 patients who were scheduled for HSCT in two comprehensive tertiary hospitals in Xuzhou and Suzhou from December 2020 to November 2021 were selected. Their general demographic and psychological data were collected using questionnaires and scales. The trend and influencing factors were analyzed by repeated measure ANOVA and generalized estimating equations. Results Patients' anxiety scores slowly decreased throughout the HSCT period, with statistical differences (P<0.05), while their depression scores slowly increased and then decreased throughout the HSCT period, with statistical differences (P<0.05). The risk factors for patients' anxiety during HSCT were religious beliefs (P=0.024) and depression (P<0.05). The risk factors for developing depression were sex (P=0.007), marriage (P=0.035) and anxiety (P=0.001), while the protective factors for developing depression were age (P=0.018), monthly household income (P=0.001) and religious beliefs (P=0.004). Conclusions The critical period for anxiety control is when the patient first enters the laminar flow room, while the myelosuppression period after undergoing chemotherapy is the critical period for depression control. Clinical nursers should strengthen the assessment of patients' anxiety and depression during HSCT based on demographic characteristics. A family-centered care model may be a new direction for psychological interventions for HSCT patients in the future.