In agriculture, crops that feed exponentially increasing populations are often exposed to harmful stresses in soil as well as in plants. These are serious pollution that can affect plant production and yield. Such stresses lead to the formation of reactive oxygen species, membrane injury, and disruption in metabolic activities within plants to reduce crop yield. To counteract these stresses, plant defense methods should be applied to restore their morpho-physiological activities and increase their yield. The advancement of nanotechnology in agriculture has gained much attention in recent years for the production of sustainable crop and abiotic stresses remediation approaches. Compared with conventional methods, the use of nanoparticles (NPs) is a very promising approach to mitigate the toxicity caused by drought and heavy metal (HM) stress in plants. NPs play important roles in seed germination, growth, photosynthesis, and antioxidant enzymes activity. In plants, NPs may be used as nanofertilizers, nano-remediators, and nanosensors, which play an important role in developing modern agricultural practices. Several studies have confirmed that NPs alter biosynthetic pathways and improve plant stress tolerance by accelerating metabolic fluxes and enhancing the cellular pool through the upregulation of enzymatic activities. Although many beneficial outputs of NPs have been described in plants, the translocation mechanism of NPs inside the cell remains unclear. In this perspective, the transportation mechanism of NPs within the plant cell and their action mechanism in the alleviation of HMs stress for sustainable crop production have been focused on in this review. In addition, authors also highlighting the NPs-mediated gene delivery towards stress tolerance.