Global warming as a result of rapid increase in atmospheric CO2 emission is significantly influencing world’s economy and human activities. Carbon sequestration in phytoliths is regarded as a highly stable carbon sink mechanism in terrestrial ecosystems to mitigate climate change. However, the response of plant phytolith-occluded carbon (PhytOC) to external silicon amendments remains unclear. In this study, we investigated the effects of basalt powder (BP) amendment on phytolith carbon sequestration in rice (Oryza sativa), a high-PhytOC accumulator. The results showed that the contents of phytolith and PhytOC in rice increased with BP amendment. The PhytOC production flux in different rice plant parts varied considerably (0.005–0.041 Mg CO2 ha−1 a−1), with the highest flux in the sheath. BP amendment can significantly enhance flux of phytolith carbon sequestration in croplands by 150 %. If the global rice cultivation of 1.55 × 108 ha had a similar flux of PhytOC production in this study, 0.61 × 107 to 1.54 × 107 Mg CO2 would be occluded annually within global rice phytoliths. These findings highlight that external silicon amendment such as BP amendment represents an effective potential management tool to increase long-term biogeochemical carbon sequestration in crops such as rice and may also be an efficient way to mitigate the global warming indirectly.