Multicolor quantum dot (QD) probes with compact sizes, excellent colloidal stability, and high quantum yields were developed by using a new class of multivalent polymer ligands based on poly(maleic anhydride) homopolymer. These size-minimized QDs allow facile construct of bioconjugated QDs through metal-affinity chelating between polyhistidine (His) tags of recombinant proteins and QD surfaces. Our results have shown that fluorescent protein, for example, mCherry with His-tag, is able to assemble on the QD surface and give rise to highly efficient fluorescence resonance energy transfer (FRET) between the QD donor and the fluorescent protein acceptor. Our results suggest that using this new class of compact QD probes leads to significant enhancement of FRET efficiency in comparison with the bulky amphiphilic polymer encapsulated QDs. We have also found that self-assembled QD probes can be successfully used for immunofluorescence cell staining, indicating that this self-assembled biotagging strategy is both versatile and robust in nature.