Triple-bond based-Raman scattering tags have attracted extensive researchers’ attention for biological multivariate labeling. However, there are still difficult to break through the “color limit”, the synthesis of signal molecules based on Raman shifts of triple bond is difficult, and the signal noise ratio of small Raman molecules is poor. In this paper, small molecular monomers containing strong triple-bond Raman scatters were rationally tailored and polymerized at the nanoscale level, which could enhance imaging contrast with smaller but brighter optical nanotags with artificial ‘fingerprint’ output. In particular, a class of triple-bond rich polymer nanoparticles (NPs) has been engineered by regulating the relative dosages of three chemically different triple-bond monomers in co-polymerization, and the suggested bonding can achieve 15 spectrally distinguishable triple-bond combinations. The accurate construction of structured nano molecular aggregates will become a universal method for small-size, high-sensitivity and high-throughput biological imaging tags for multi-color imaging.