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The objective of this study was to identify novel acetylation (Ac) modifications of the C1-inhibitor (C1-INH) and explain the association of the levels of autoantibodies against acetylated C1-INH peptides with the risk of developing systemic lupus erythematosus (SLE). Ac modifications of the C1-INH were identified and validated through in-gel digestion, nano-liquid chromatography-tandem mass spectrometry, immunoprecipitation, and Western blotting by using serum protein samples obtained from patients with SLE and age-matched healthy controls (HCs). In addition, the levels of serum C1-INH, Ac-protein adducts, and autoantibodies against unmodified and acetylated C1-INH peptides were measured. C1-INH levels in patients with SLE were significantly lower than those in HCs by 1.53-fold (<i>p</i> = 0.0008); however, Ac-protein adduct concentrations in patients with SLE were significantly higher than those in HCs by 1.35-fold (<i>p</i> = 0.0009). Moreover, immunoglobulin M (IgM) anti-C1-INH^{367&#8722;385} Ac and IgA anti-C1-INH^{367&#8722;385} Ac levels in patients with SLE were significantly lower than those in HCs. The low levels of IgM anti-C1-INH^{367&#8722;385} (odds ratio [OR] = 4.725, <i>p</i> &lt; 0.001), IgM anti-C1-INH^{367&#8722;385} Ac (OR = 4.089, <i>p</i> = 0.001), and IgA anti-C1-INH^{367&#8722;385} Ac (OR = 5.566, <i>p</i> &lt; 0.001) indicated increased risks for the development of SLE compared with HCs.