Objective: There is substantial evidence to support that the alterations in the immune-inflammation system play a crucial role in the pathogenic mechanism of affective disorders. The neutrophil/lymphocyte ratio (NLR), platelet/lymphocyte ratio (PLR) and monocyte/lymphocyte ratio (MLR) have been recently investigated as simple, rapid, and inexpensive inflammation markers. The purpose of the research is to use large-scale clinical data to study the difference of the inflammation ratios in first-episode MDD, recurrent MDD, BD depressive episodes and manic episode. Methods: A cross-sectional design was applied to retrospectively analyse the data that were extracted from electronic health records. A total of 16,174 Chinese affective disorder patients were enrolled in this study, and 6681 healthy subjects served as controls. The differences in the NLR, MLR, PLR and whole blood count data among different groups were compared, and the contributing factors for the occurrence of MDD and BD were analysed. Results: First-episode and recurrent MDD patients exhibited significantly elevated NLRs and MLRs compared to healthy controls. Compared with the MDD patients, the BD patients showed higher NLRs and MLRs and lower PLRs. Further analysis showed that the BD manic episode patients had significantly elevated NLRs and MLRs compared to patients with BD depressive episodes or MDD. MLR was a risk factor for the occurrence of MDD and that the NLR and MLR were risk factors for the occurrence of BD. Conclusions: Our study highlights the role of systemic inflammation in the pathophysiology of MDD and BD, particularly during manic BD episodes.