Abstract: As an efficient monitoring and prediction tool, chemical tracers have been widely applied in reservoir characterization, production monitoring, water resources monitoring, and various other fields. Chemical tracer technology is characterized by high efficiency, high precision, relatively simple operational procedures, and low cost. Owing to the limitations of existing tracers, such as minimal options, limited transport efficiency, and complex detection methods, this study used fluorescein isothiocyanate and a ruthenium complex (Ru(phen3)2+) to synthesize 50 nm multi-color fluorescent silica nanoparticle tracers using an improved Stöber method based on fluorescence resonance energy transfer (FRET). Due to the FRET between the two compounds, the synthesized tracer exhibited the characteristics of multi-color fluorescence, and its fluorescent color varied with the mixing ratio of the two precursor solutions. The fluorescence intensity of the synthesized tracer was significantly higher than that of the monochromatic fluorescent nano-tracer. Fourier-transform infrared spectroscopy, ultraviolet spectrophotometry, and fluorescence spectrometry were used to characterize the structure, maximum absorption wavelength, and fluorescence characteristics of the synthesized tracer, respectively. The experimental results show that the synthesized tracer has a maximum absorption wavelength of 450 nm and an emission wavelength of 576 nm. Under field emission scanning electron microscopy, the tracer appears as uniformly spherical particles with a size of 50 ± 5 nm. It exhibited good dispersibility and fluorescence characteristics in reservoir environments that varied in temperature (25–85 °C) and salinity (1000–10000 mg/L). The effects of environmentally sensitive clay minerals, tracer particle size, injection concentration, fluid salinity, and flow rate on the transport characteristics (retention) of tracers in sandstone cores were studied using 12 sets of tracer breakthrough experiments. The experimental results showed that increased sensitivity to clay minerals, salinity, and tracer particle size were not conducive to tracer migration in the core. In contrast, increased tracer injection concentration and flow rate were beneficial to tracer migration in the core.