The prevalence of toxic element thallium (Tl) in soils is of increasing concern as a hidden hazard in agricultural systems and food chains. In the present work, pure biochar (as a comparison) and jacobsite (MnFe2O4)-biochar composite (MFBC) were evaluated for their immobilization effects in Tl-polluted agricultural soils (Tl: similar to 10 mg/kg). Overall, MFBC exhibited an efficient effect on Tl immobilization, and the effect was strengthened with the increase of amendment ratio. After being amended by MFBC for 15 and 30 days, the labile fraction of Tl in soil decreased from 1.55 to 0.97 mg/kg, and from 1.51 to 0.88 mg/kg, respectively. In addition, pH (3.05) of the highly acidic soil increased to a maximum of 3.97 after the immobilization process. Since the weak acid extractable and oxidizable Tl were the preponderantly mitigated fractions and displayed a negative correlation with pH, it can be inferred that pH may serve as one of the most critical factors in regulating the Tl immobilization process in MFBC-amended acidic soils. This study indicated a great potential of jacobsite-biochar amendment in stabilization and immobilization of Tl in highly acidic and Tl-polluted agricultural soils; and it would bring considerable environmental benefit to these Tl-contaminated sites whose occurrence has significantly increased in recent decades near the pyrite or other sulfide ore mining and smelting area elsewhere.