Soil degradation and pollution pose significant threats to global agricultural sustainability and food security. Conventional remediation methods are often constrained by low efficiency, high cost, and potential secondary pollution. Nanobiotechnology, an emerging interdisciplinary field, offers innovative solutions by integrating functional nanomaterials with plant–microbe interactions to advance soil remediation and sustainable agriculture. This review systematically elaborates on the mechanisms and applications of nanomaterials in soil remediation and enhanced plant stress resilience. For contaminant removal, nanomaterials such as nano-zero-valent iron (nZVI) and carbon nanotubes effectively immobilize or degrade heavy metals and organic pollutants through adsorption, catalysis, and other reactive mechanisms. In agriculture, nanofertilizers facilitate the regulated release of nutrients, thereby markedly enhancing nutrient use efficiency. Concurrently, certain nanoparticles mitigate a range of abiotic stresses—such as drought, salinity, and heavy metal toxicity—through the regulation of phytohormone balance, augmentation of photosynthetic performance, and reinforcement of antioxidant defenses. However, concerns regarding the environmental behavior, ecotoxicity, and long-term safety of nanomaterials remain. Future research should prioritize the development of smart, responsive nanosystems, elucidate the complex interactions among nanomaterials, plants, and microbes, and establish comprehensive life-cycle assessment and standardized risk evaluation frameworks. These efforts are essential to ensuring the safe and scalable application of nanobiotechnology in environmental remediation and green agriculture.