Heat stress is an environmental challenge that reduces plant productivity and growth. Plants have developed corresponding mechanisms to survive this adverse environmental stress. To demonstrate the mechanisms of how plants adapt to the environmental challenge, the heat response experiments involving Arabidopsis thaliana were retrieved from the GEO database. After quantile normalization of the GEO raw data, the differentially expressed genes (DEGs) in response to heat stress were identified by robust rank aggregation (RRA) algorithm, including 384 up-regulated and 302 down-regulated genes. Then, systematic bioinformatics analyses disclosed that the up-regulated DEGs were mainly related to protein refolding, abscisic acid catabolic process, potassium ion import, response to hydrogen peroxide, cytochrome complex assembly, and apoptotic process, and the down-regulated DEGs were involved in microsporocyte differentiation, syncytium formation, adventitious development, glutathione metabolism, and glycine metabolic process. The up-regulated DEGs also had more complicated PPI interactions than the down-regulated DEGs, and potential core genes of heat stress tolerance were provided. Furthermore, the mRNA expression of core genes Hsp70-2 (At5g02490), Hsp70-3 (At3g09440), and Hsp70-4 (At3g12580) has been measured to validate the outcome of integrated bioinformatics analysis. Our work will extend our understanding of heat-responsive mechanisms and these DEGs might be potential markers for plant heat stress-resistance studies.