Salinity stress is a major constraint on plant organ morphogenesis, and agricultural production, mostly by disrupting ion homeostasis and plant water status, leading to detrimental K+/Na+ imbalance. Maintaining subcellular ionic balance is a critical defense mechanism against abiotic stresses, and plants employ diverse strategies to mitigate ion toxicity. Nanobiotechnology offers a promising approach to enhance plant ion homeostasis under stressed environments, leveraging nanoparticles' (NPs) capacity to modulate stress-responsive signaling pathways in crops. Crucially, NPs initiate crosstalk between Ca²⁺ signaling and hormonal networks, which cooperate with reactive oxygen species (ROS), K+, and nitric oxide (NO) signaling to regulate transcription factors (TFs) essential for ionic equilibrium. This review examines the role of NPs in promoting K⁺/Na⁺ homeostasis during salinity stress by regulating molecular, physiological, anatomical, and morphological mechanisms. These NP-induced Ca²⁺/hormonal networks directly or indirectly regulate NO signaling to bolster organ morphogenesis and stress tolerance. NPs enhance salinity tolerance by upregulating key genes (e.g., SOS1, SOS2, SOS3, HKT1, NHX), improving ion homeostasis and organ development. Moreover, NP-triggered crosstalk between Ca²⁺ signaling and hormones plays a pivotal role in regulating TFs such as bHLH, R2R3-MYB, WRKY, NAC, ZIP, ERFs, and NFX1. Collectively, these signaling and TF networks orchestrated by NPs sustain a high K⁺/Na⁺ ratio by regulating K⁺ and Ca²⁺ transport/distribution and reducing Na⁺ toxicity. Improved K⁺/Na⁺ regulation enhances nutrient uptake, activates ROS scavenging systems, modulates phytohormone levels, boosts photosynthetic efficiency, and optimizes stomatal motions. Understanding the mechanistic basis of NP-mediated stress regulation will elucidate their mode of action and the associated signaling cascades, clarifying their contribution to ion homeostasis under salinity stress.