•Amendment of either B or Si significantly alleviated Cd accumulation and toxicity in hydroponically-cultured rice plants.•There existed strong interaction between the two elements in rice tolerance to Cd toxicity.•Addition of B and Si alleviated Cd-induced oxidative stress by improving antioxidative systems.•Supplement of B and Si in Cd-treated plants downregulated the expression of Cd transporter genes. Cadmium (Cd) is a highly toxic heavy metal for both animals and plants. Rice consumption is a major source of Cd intake for human. Minimization of Cd accumulation in rice is key to reduce Cd hazard to human. Here we showed alleviating effects of boron (B), silicon (Si) and their mixture on Cd accumulation and toxicity in hydroponically-cultured rice plants. Cd treatment (100 μM) led to Cd accumulation in roots and shoots, as well as significant reduction in plant growth. However, amendment of either B or Si significantly alleviated Cd accumulation and toxicity. Moreover, simultaneous supply of B and Si showed better alleviating effect. However, addition of B and Si alleviated Cd-induced oxidative stress in Cd-treated plants as reflected by reduced MDA, H2O2 and O2−, as well as increased activities of major antioxidant enzymes. Cd exposure induced the expression of Cd transporter genes of OsHMA2, OsHMA3, OsNramp1 and OsNramp5. In contrast, simultaneous supplement of B and Si in Cd-treated plants compromised the gene expression. Our results show that both B and Si alleviate Cd accumulation and toxicity by improving oxidative stress and suppressing Cd uptake and transport, and the two elements display joint effect.