Functional gene expression is a basic life process that connects coding information of a gene to protein products. The level of gene expression is considered as a quantitative trait between genotype and phenotype and plays an important role in plants response to climatic and environmental changes. First, this review systematically comments on regulatory elements of gene expression in plant species and empirical evidence, including the effects of transcription factors and small RNAs on gene expression regulation. Secondly, this review discusses the eQTLs mapping for regulatory elements of gene expression through gene expression-based GWAS analysis and the limitations of this method. This review then analyzes the intraspecific variation of gene expression in theory under the processes of mutation, drift and selection and the testing methods. The review also analyzes the interspecific evolution of gene expression under the mutation and drift processes or under the phylogeny-based drift-selection processes, and the testing methods. Finally, the review discusses the regulation of gene expression by plant mating system. Selfing reduces effective population size, mutation rate, recombination rate and the competition from exogenous pollen, and changes the efficacy of natural selection in gametophytic and sporophytic phases. Selfing regulates intraspecific gene expression variation and interspecific gene expression evolution. The whole review comprehensively comments on theoretical and practical research progress and existing questions, which aids in our deep understanding of plant gene expression regulation and evolution mechanisms.