Epigenetic modifications, like high DNA methylation levels and low histone acetylation levels, are the main explanations for transcriptional suppression, which has a regulative role in secondary metabolites-related gene expression. Most of the secondary metabolites (SMs) biosynthesis pathways are epigenetically controlled through the evolutionary stages. It has been theorized that Chemical epigenetic modifiers such as 5-azacitidine can effectively manipulate the morphological changes as well as the production of SMs. However, far too little attention has been paid to understanding the potential roles of epigenetics on both cannabis chemodiversity and morphology. This research aims to enhance the production of cannabis-specialized metabolites such as cannabinoids and terpenes using epigenetic modifiers. We conducted a within-chamber experiment in which we treated cannabis cuttings with four different concentrations of 5-azacytidine and examined the consequences of this treatment for their phenotypic changes as well as secondary metabolites profile. Results showed a significant reduction in dry and fresh biomass, head flowers, height, and root biomass between controls and treatments. However, no changes in cannabinoid profile were observed. Having a comprehensive insight into epigenetic modifiers and their impact on gene expression might help to manipulate the cannabis secondary metabolite profile in the future.