ObjectivePrevious studies have partly discussed the roles of inflammatory cytokines in obesity and systemic lupus erythematosus (SLE), but the causal relationship among inflammatory cytokines, obesity, and SLE is unclear. It is challenging to comprehensively evaluate the causal relationship between these variables. This study aimed to investigate the role of cytokines as intermediates between obesity and SLE.MethodsThe inverse‐variance weighted method (IVW) of mendelian randomization (MR) is mainly used to explore the causal relationship between exposure and outcome by using the genetic variation of the open large genome‐wide association studies (GWAS), namely single‐nucleotide polymorphisms (SNPs) related to obesity (more than 600 000 participants), inflammatory cytokines (8293 healthy participants) and SLE (7219 cases). Methods such as weighted median, MR‐Egger are used to evaluate the reliability of causality. Reverse analysis is performed for each MR analysis to avoid reverse causality. Cochran's Q statistic and funnel chart are used to detect heterogeneity, MR‐Egger intercept test and leave‐one‐out sensitivity analyses evaluated pleiotropy.ResultsObesity was associated with 25 cytokines, and 3 cytokines were associated with SLE, including CTACK (OR = 1.19, 95% CI: 1.06, 1.33, p = .002), IL‐18 (OR = 1.13, 95% CI: 1.01, 1.26, p = .027), SCGFb (OR = 0.89, 95% CI: 0.79, 0.99, p = .044). In the opposite direction, SLE was associated with 18 cytokines, and 2 cytokines were associated with obesity, including IP‐10 (βIVW = −.03, 95% CI: −0.05, −0.01, p = .002), MIP‐1B (βIVW = −.03, 95% CI: −0.05, −0.01, p = .004).ConclusionOur MR study suggested that CTACK, IL‐18 and SCGFb may play an intermediary role in obesity to SLE, while IP‐10 and MIP‐1B may play an intermediary role in SLE to obesity.