The physical properties of nano-fertilizers (NFs) are important in determining their performance, efficacy, and environmental interactions. Nano-fertilizers, due to their small size and high surface area-to-volume ratio, enhance plant metabolic reactions, resulting in higher crop yields. The properties of nano-fertilizers depend on the synthesis methods used. The nanoparticle’s nutrient use efficiency (NUE) varies among plant species. This review aims to analyze the relationship between the physical properties of NF and their influence on crop performance and nutrient uptake efficiency. The review focuses on the physical properties of NFs, specifically their size, shape, crystallinity, and agglomeration. This review found that smaller particle-sized nanoparticles exhibit higher nutrient use efficiency than larger particles. Nano-fertilizer-coated additives gradually release nutrients, reducing the need for frequent application and addressing limitations associated with chemical fertilizer utilization. The shapes of nano-fertilizers have varying effects on the overall performance of plants. The crystalline structure of nanoparticles promotes a slow release of nutrients. Amorphous nano-fertilizers improve the NUE and, ultimately, crop yield. Agglomeration results in nanoparticles losing their nanoscale size, accumulating on the outer surface, and becoming unavailable to plants. Understanding the physical properties of nano-fertilizers is crucial for optimizing their performance in agricultural applications.