Temperatures that extend beyond normal levels of tolerance cause severe stress to plants, especially during the reproductive and grain filling/ripening stages. Heat stress leads to serious yield losses in many crop plants, including rice (Oryza sativa). In view of the current scenario of global climate change, frequent fluctuations and a significant increase in average temperatures will pose challenges to protecting those yields. Therefore, elucidating the molecular mechanisms that make crop plants more tolerant of heat, particularly in organs at the reproductive stage, is of utmost importance. Precise molecular information will be helpful for the manipulation and exploration of relevant genes for use in crop improvement programs. In this review, we highlight recent progress in research on the molecular responses to high temperatures in pollen and seed and provide a perspective on the development of heat tolerance in rice cultivars. The responsible mechanism is a very complex phenomenon that involves several biochemical and physiological changes, molecular responses, and a series of signal transductions. Improving our understanding requires detailed knowledge at various omics levels. Recent technological advancements have accelerated genomics, transcriptomics, and proteomics studies in rice, a model crop plant. Here, we discuss those technological and omics approaches being taken to investigate the heat tolerance mechanism, particularly in rice. In addition, we address the tools being used to identify key genes and QTLs that can then be utilized for molecular breeding and biotechnology.