The concept of synergistic effects has been widely applied in many scientific fields such as in biomedical science and material chemistry, and has further attracted interest in the fields of both synthesis and application of nanomaterials. In this paper, we report the synthesis of long-wavelength emitting silicon quantum dots based on a one-step hydrothermal route with catechol (CC) and sodium citrate (Na-citrate) as a reducing agent pair, and N-[3-(trimethoxysilyl)propyl]ethylenediamine (DAMO) as silicon source. By controlling the reaction time, yellow-emitting silicon quantum dots and green-emitting silicon quantum dots were synthesized with quantum yields (QYs) of 29.4% and 38.3% respectively. The as-prepared silicon quantum dots were characterized by fluorescence (PL) spectrum, UV–visible spectrum, high resolution transmission electron microscope (HRTEM), Fourier transform infrared (FT-IR) spectrometry energy dispersive spectroscopy (EDS), and Zeta potential. With the aid of these methods, this paper further discussed how the optical performance and surface characteristics of the prepared quantum dots (QDs) influence the fluorescence mechanism. Meanwhile, the cell toxicity of the silicon quantum dots was tested by the 3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium (MTT) bromide method, and its potential as a fluorescence ink explored. The silicon quantum dots exhibit a red-shift phenomenon in their fluorescence peak due to the participation of the carbonyl group during the synthesis. The high-efficiency and stable photoluminescence of the long-wavelength emitting silicon quantum dots prepared through a synergistic effect is of great value in their future application as novel optical materials in bioimaging, LED, and materials detection.