This study investigated the influence of high temperature on the expression patterns of multiple DBE isoform genes (PUL, ISA1, ISA2 and ISA3) at RNA transcriptional level in developing endosperm, as well as its relation to the varying total activity of DBE and starch fine structure. Two rice genotypes with different amylose content and palatability were used for research under two temperature treatments (32°C and 22°C for the mean daily temperature, respectively) at filling stage. The temperature treatments were laid out in a completely randomized design. The data were analyzed using SPSS into one-way ANOVA, and means separation was carried out with the LSD method The result showed that high temperature resulted in the decrease of DP5-9 and DP15-22, and increase of DP10-13 and DP>42 of amylopectin in rice endosperm. For enzyme activity, PUL and ISA showed higher activities at initial stage, but substantially lower at later filling stage relative to low temperature. For different DBE isoform genes, ISA1 and ISA2 presented up-regulation pattern at high temperature over the whole sampling stage, while ISA3 and PUL showed the opposite case at the later filling stage in comparison of their corresponding low temperature. The DBEs isozyme activities and their transcriptional expression indicated that ISA2 was one of the dominant DBE isoforms highly expressed at later filling stage. The contribution of ISA3 expression to total ISA activity was mostly at earlier filling stage when rice plants were subjected to high temperature. Further investigations are required to elucidate the coordinated action of multiple key enzymes in starch synthesis at high temperature and their relations to amylopectin fine structure and rice quality.