Introduction The present study aimed to investigate the prevalence and influential factors of thrombocytopaenia in systemic lupus erythematosus (SLE) patients among the Chinese population in order to provide evidence for improving the treatment and nursing of SLE patients. Methods A retrospective analysis of 3140 SLE patients admitted to two large tertiary hospitals was conducted in Anhui, China, from 2011 to 2018. In addition, the influential factors related to SLE with thrombocytopaenia were analysed through univariate and multivariate analysis. Results A total of 804 SLE patients had thrombocytopaenia (25.6%). The top 5 clinical manifestations of SLE inpatients were proteinuria (51.0%), lupus nephritis (45.9%), new rash (38.4%), haematuria (36.7%) and pyuria (32.2%). The incidence of neurological manifestations, oral mucosal ulceration, pleurisy, pericarditis, hyperglycaemia, leucocytopaenia, urinary casts, haematuria, pyuria and high disease activity in the thrombocytopaenia group were higher than those in the non-thrombocytopaenia group ( p < 0.05). Multivariate analysis showed age (odds ratio (OR) = 1.009, p = 0.005), neurological manifestations (OR = 1.373, p = 0.048), pericarditis (OR = 1.394, p = 0.048), hyperglycaemia (OR = 1.717, p < 0.001), leucocytopaenia (OR = 2.551, p < 0.001), haematuria (OR = 1.582, p < 0.001), serum C3 level <0.85 g/L (OR = 1.525, p = 0.001), serum C4 concentration <0.10 g/L (OR = 1.287, p = 0.020), serum CRP concentration <8 ng/L (OR = 1.314, p = 0.005), prothrombin time >15.30 seconds (OR = 1.479, p = 0.032), activated partial thromboplatin time >45 seconds (OR = 1.924, p < 0.001) and thrombin time >21 seconds (OR = 1.629, p = 0.015) were associated with thrombocytopaenia. Conclusion Thrombocytopaenia has a high prevalence in SLE patients and is related to some baseline, clinical and laboratory characteristics, affecting multiple organs and systems.