The ratiometric fluorescence technique is of great interest due to its visualization characteristics. The construction of a reliable fluorescent ratiometric nanoprobe for high-sensitivity visual quantification is highly sought after but it is limited by poor stability and controllability. Herein, we report a robust dual-emissive quantum dot nanohybrid with precise color tunability and demonstrate its potential as a two-signal-change ratiometric probe for visual detection. A novel assembly strategy was developed for spatially implanting hydrophobic green and red quantum dots (QDs) into a silica scaffold to form a dual-emissive hierarchical fluorescent silica nanohybrid. The fluorescence intensity ratio and color of the nanohybrid were precisely tailored by altering the amounts of green and red QDs. Particularly, after the alkylsilane-mediated phase transfer and exterior silica shell growth, the nanohybrid exhibited the well-preserved fluorescence features of the original QDs and robust optical/colloid stability. An inner filter-based ratiometric nanoprobe for the visual determination of melamine was ultimately devised by combining the spectra-overlapped two-colored fluorescent nanohybrid with analyte-specific gold nanoparticles. Furthermore, based on the reversible fluorescence signal changes in two-colored QDs induced by melamine, a logic gate strategy for melamine monitoring was constructed. The newly developed fluorescent ratiometric nanoprobe shows great prospects for the visual and quantitative determination of analytes in a complex biological matrix.