Background: Huntington’s disease (HD) poses a significant socio-economic burden globally. Existing research on HD’s economic burden predominantly comes from Western settings, leaving a gap in data from Asian countries. This study aimed to assess the economic burden of HD in China and identify cost-driving factors. Methods: This study used data from a 2019 nationwide cross-sectional survey of individuals affected by rare diseases in China. Data included socio-demographic characteristics, income, disease stage, health and social insurance coverage status, treatment-seeking behaviour, and costs. Logistic regression and linear regression were used to explore potential contributors to treatment-seeking behaviour and associated costs. Results: Of the 269 individuals with HD included in this study, 80.6% were actively seeking treatment. The average annual direct medical cost, direct non-medical cost, and indirect cost were 3,265.65, 805.82, and 801.97 Euros, respectively. Compared to participants with early-stage HD, those with middle- or advanced-stage HD reported higher direct medical costs (coefficient 1,612.70, 95% confidence interval [CI]: [141.92, 3,083.48] and 2,398.58, 95% CI: [791.16, 4,006.00], respectively). However, the disease stage was not significantly associated with direct non-medical costs or indirect costs. Conclusions: This study provides crucial insights into the economic burden of HD in China. It emphasises a need for targeted policies that better cater to the financial needs of HD patients.