Microplastics and nanoplastics (MNPs), defined as plastic fragments, fibers, and particles with diameters below 5 mm and 1 μm, respectively, are widely spread emerging contaminants in soil environments. Due to frequent material exchanges within the soil–plant system, MNPs can be transferred from soil into plants, accumulate and distribute across various plant tissues, and thus pose a potential threat to the health of the soil–plant system. MNPs can significantly alter soil physicochemical properties and migrate from soils into plant tissues, leading to adverse effects on plant growth and physiological-biochemical functions. To overcome the limitations imposed by the complexity of the environmental matrix, advanced labeling techniques provide a fast and efficient way for visually tracking and quantifying MNPs in soil-plant systems, which are essential for deepening mechanistic understanding. This review systematically evaluates four mainstream labeling methods. Fluorescent labeling is cost-effective and easy to implement, but limited by photobleaching and interference from environmental matrices. Metal-based labeling combined with inductively coupled plasma mass spectrometry (ICP-MS) allows for stable quantification, though it may change the physicochemical properties of MNPs. Stable isotope labeling (such as ¹³C or ¹⁵N) provides high specificity for tracing degradation pathways but faces challenges due to technical complexity and background signals as well. Radioisotope labeling (e.g., ¹⁴C, ³H) offers ultrahigh sensitivity but raises concerns regarding environmental biosafety and high costs. On this basis, this paper focuses on introducing rare earth element labeling technology, which uses the fluorescence properties of lanthanide chelates and their quantifiable characteristics to simultaneously realize visual tracing and precise quantification of MNPs. It is particularly suitable for studying environmental behavior and food chain transmission risks of MNPs in soil-plant systems. In the future, new markers that are more precise and efficient should be developed, and new labeling technologies that combine multiple labeling methods should be developed to more systematically and comprehensively reveal the environmental fate and ecological risks of MNPs, and provide a scientific basis for pollution control of MNPs in soil-plant systems.