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Several articles have reported a high prevalence of thyroid disease in SSc patients, while one study suggested a potential contribution of appendicitis to the development of SSc. To investigate this causal association, we conducted Mendelian randomization (MR) analysis using instrumental variables (IVs) to assess exposure and outcome. In the MR study involving two cohorts, all analyses were conducted using the TwoSampleMR package in R (version 4.3.0). Single nucleotide polymorphisms (SNPs) meeting a statistically significant threshold of 5E\u221208 were included in the analysis. Multiple complementary approaches including MR-IVW, MR-Egger, weighted median, simple mode, and weighted mode were employed to estimated the relationship between the exposure and outcome. Leave-one-out analysis and scatter plots were utilized for further investigation. Based on the locus-wide significance level, all of the MR analysis consequences manifested no causal association between the risk of appendicitis with SSc (IVW OR 0.319, 95% CI 0.063\u201314.055, <jats:italic>P<\/jats:italic>\u2009=\u20090.966). Negative causal effects of autoimmune thyroiditis (AT) on SSc (IVW OR 0.131, 95% CI 0.816\u20131.362, <jats:italic>P<\/jats:italic>\u2009=\u20090.686), Graves\u2019 disease (GD) on SSc (IVW OR 0.097, 95% CI 0.837\u20131.222, <jats:italic>P<\/jats:italic>\u2009=\u20090.908), and hypothyroidism on SSc (IVW OR 1.136, 95% CI 0.977\u20131.321, <jats:italic>P<\/jats:italic>\u2009=\u20090.096) were derived. The reverse MR revealed no significant causal effect of SSc on thyroid disease. According to the sensitivity analysis, horizontal pleiotropy was unlikely to distort the causal estimates. The consequences indicated no significant association between AT, GD, and hypothyroidism with SSc. 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