We investigated heat shock (HS)‐triggered Ca2+ signalling transduced by a Ca2+ sensor, calmodulin (CaM), linked to early transcriptome changes of HS‐responsive genes in rice. We observed a biphasic [Ca2+]cyt signature in root cells that was distinct from that in epicotyl and leaf cells, which showed a monophasic response after HS. Treatment with Ca2+ and A23187 generated an intense and sustained increase in [Ca2+]cyt in response to HS. Conversely, treatment with Ca2+ chelator, L‐type Ca2+ channel blocker and CaM antagonist, but not intracellular Ca2+ release inhibitor, strongly inhibited the increased [Ca2+]cyt. HS combined with Ca2+ and A23187 accelerated the expression of OsCaM1‐1 and sHSPC/N genes, which suggests that the HS‐induced apoplastic Ca2+ influx is responsible for the [Ca2+]cyt response and downstream HS signalling. In addition, the biphasic response of OsCaM1‐1 in the nucleus followed the Ca2+ signature, which may provide the information necessary to direct HS‐related gene expression. Overexpression of OsCaM1‐1 induced the expression of Ca2+/HS‐related AtCBK3, AtPP7, AtHSF and AtHSP at a non‐inducing temperature and enhanced intrinsic thermotolerance in transgenic Arabidopsis. Therefore, HS‐triggered rapid increases in [Ca2+]cyt, together with OsCaM1‐1 expression and its nuclear localization, are important in mediating downstream HS‐related gene expression for the acquisition of thermotolerance in rice.