Aim Olfactory deficits are potential markers of early diagnosis, monitoring progress and predicting outcome in patients with schizophrenia and depression. We aimed to investigate differences in patterns and influencing factors of olfactory deficits between patients with acute episode of schizophrenia and major depressive episode (MDE). Methods: Fifty-two patients with acute episode of schizophrenia, 75 patients with unipolar MDE and 199 healthy controls were included in this retrospective study. Following a structured interview, participants underwent olfactory tests (Sniffin' Sticks), assessment of psychiatric symptoms (Positive and Negative Syndrome Scale), depressive symptoms (Hamilton Depression Rating Scale), and cognitive function (color-word test and word generation test). Results: Both patients with schizophrenia and MDE exhibited significant olfactory deficits, and MDE patients have poorer olfactory sensitivity than schizophrenia. Patients with MDE had a higher proportion of olfactory deficits (45.3% and 28%, respectively) but a better self-awareness (21.3% and 9.6%, respectively) than patients with schizophrenia. In patients with schizophrenia, PANSS scores was positively associated with olfactory sensitivity but negatively associated with olfactory identification, and olfactory discrimination was associated with word generation. In patients with MDE, olfactory discrimination was associated with word generation and age, but not disease severity. First-episode schizophrenia group showed significantly lower threshold scores than recurrent schizophrenia group, and first-episode MDE group had significantly lower threshold scores and higher discrimination scores than the recurrent MDE group. Conclusions: Patterns and modulating factors of olfactory deficits in acute episode of schizophrenia and MDE are different, their differences should be considered when using olfactory deficits as marker in clinical practice.