Previous observational studies have suggested that hypothyroidism may affect the risk of cancer. However, the causal effects were still unclear and controversary. Therefore, a two-sample Mendelian randomization (MR) analysis was conducted to evaluate the association between hypothyroidism and six types of cancer, including colorectum, pancreas, prostate, lung, bladder and stomach cancer. The inverse variance weighted (IVW), MR-Egger and Weighted Media were carried out to estimate the relation in the MR analysis. Different approaches such as leave-one-out analysis and MR-PRESSO for sensitivity analyses were used to assess the stability of the results. The MR results showed that hypothyroidism was causally associated with decreased risk of lung cancer (OR [odds ratio] = 0.19, P= 0.007), colorectal cancer (OR = 0.27, P= 0.016) and prostate cancer (OR = 0.18, P= 7.44e-05). Significant association between hypothyroidism and the risk of bladder cancer, stomach cancer and pancreas were not found with IVW P>0.05. These results indicated that hypothyroidism can decrease the risk of lung cancer, colorectal cancer and prostate cancer. But evidence of the association between hypothyroidism and other three types of cancer was not found in our study. Further research is necessary to clarify the relation.