Manganese (Mn) is an essential micronutrient for plant growth. However, in acidic paddy fields, rice is susceptible to Mn toxicity, which triggers excessive Mn accumulation in plant tissues and disrupts micronutrient homeostasis. These adverse effects further inhibit rice growth and induce oxidative stress. This study aimed to investigate the differences in Mn toxicity tolerance among different rice subspecies and the regulatory mechanism of silicon (Si). The growth responses of japonica and indica rice subspecies to high Mn stress and the mitigating effect of Si were compared. The results showed that high Mn stress significantly inhibited rice growth, with plant biomass decreasing by 1.37%–63.67% compared with the control. Moreover, indica rice was more sensitive to Mn toxicity, with tissue Mn content 1.90%–52.28% higher than that of japonica rice. The addition of Si significantly increased rice biomass, but the alleviation magnitude was lower in indica than in japonica. Meanwhile, Si application reduced plant Mn concentration by 1.33%–29.34%. In addition, Si markedly decreased the concentrations and translocation to shoots of Fe, Zn, Cu and other trace elements. In conclusion, indica rice exhibits higher sensitivity to Mn toxicity, which may be associated with higher Mn accumulation. Si effectively alleviates the growth inhibition caused by Mn toxicity by reducing the accumulation and translocation of Mn and other trace elements in rice. This study provides a theoretical basis for revealing the mechanism of Si-mediated alleviation of Mn toxicity and for screening Mn-tolerant rice varieties.