A class of organic, naturally occurring compounds known as phytohormones affects physiological functions in plants at trace levels. Phytohormones play important roles in plant growth, development, nutrient transport, and survival by regulating plant responses to abiotic stress and form the basis of ability of plants for adapting to changing conditions. To carry out some specific and distinct functions, cells of complex organisms implement gene regulation dynamics according to their cell types, including during the synthesis and control of various plant hormones. Rather than the traditional approaches for phytohormone quantification, single-cell RNA sequencing (scRNA-seq) and/or single-nucleus RNA sequencing (snRNA-seq) technologies that enable high-resolution mapping of cellular heterogeneity at the transcriptomic level, provide a novel approach for the phytohormone signaling. Here, we detailed the methodology of single cell/nucleus technologies to investigate underlying gene regulatory networks of plant hormone biology.