Background Hypothyroidism is a key manifestation of autoimmune thyroid disease (AITD). Our previous research has found that low selenium (Se) status was linked to an elevated prevalence and incidence of thyroid diseases. We hypothesized that Se status may also influence the restoration of thyroid function. Thus, our study aims to investigate the factors affecting the recovery of thyroid function in patients with (sub-)clinical hypothyroidism, with a specific focus on Se status.Methods We conducted a 6-year prospective cohort study comparing different Se concentration regions. Demographic and disease data were collected from 1190 subjects (549 Se-adequate and 641 Se-deficient), who successfully completed the follow-up study in 2019. Additionally, urinary iodine (I) levels, thyroid function, and serum and nail Se levels were measured. We used logistic regression to investigate the relationship between Se deficiency and thyroid function recovery.Results Two counties were similar in sex, smoking status. The recovery rate of thyroid function was significantly higher in Se-deficient counties (46.0% vs. 30.6%, P = 0.008). In multivariate analysis, our results show that female sex [OR (95%CI) = 1.977 (1.279–3.055), P = 0.002] and increasing age [OR (95%CI) = 1.027 (1.007–1.047), P = 0.007] were associated with the recovery rate. Additionally, our study revealed that while the Se status was significant in univariate analysis, this association appeared to fade in multivariate analysis.Conclusions Female sex and increasing age have unfavorable effects on the recovery of thyroid function in patients with (sub-)clinical hypothyroidism who are over 30 years old.