Plant physiology is influenced by a combination of internal and external factors that have led to remarkable diverse functions. Recent progress in understanding the proximate basis of plant physiology has revealed a myriad of underlying mechanisms, ranging from genomics and epigenomics to transcriptomics, proteomics, and metabolomics. This Special Issue called for review or research articles, short letters, and reports that provided novel insights into plant physiological mechanism research. It is centered around timely topics, including the molecular and physiological mechanisms of character improvement, responses to biotic and abiotic stresses, hormonal and environmental signaling, and postharvest. We welcomed research using cutting-edge technologies, such as genomics, ATAC-seq, and genome editing. We encouraged the publication of research papers with significant innovative technologies and creative ideas related to plant physiology. In addition, we invited experts in plant physiology to write up-to-date review articles that highlight recent advances and future perspectives.