Eliminating colloidal toxicity and enabling its intrinsic fluorescence in aggressive environmental conditions are the key challenges for commercializing hydrophobic cadmium based quantum dots (QD). Polyarylene ether nitriles (PEN) are an example of super-engineering thermoplastics that possess a unique combination of thermal stability, intrinsic fluorescence, biocompatibility and distinct emulsion self-assembly feature. Herein, the co-self-assembly of amphiphilic PEN with hydrophobic CdSe@ZnS QD, confined in the three-dimensional (3D) oil-in-water emulsion droplets, has been explored to fabricate fluorescent microparticles (FMP). It was found that these FMP demonstrated good biocompatibility (cell viability above 90%), while exhibiting a fluorescence emission in aqueous solution that was retained (intensity retention ratio above 80%) within the whole pH range of 1-14, as well as, after being subjected to autoclaving at 120 ^oC for 1 h. Interestingly, it was discovered that introduction of calcium ions in the emulsion self-assembly contributed to in-situ generation of phase changing nanoplates inside the FMP, which led to the photo-thermal modulated solid state fluorescence from drop-casted FMP film. Thanks to their versatile fluorescence, these FMP colloids were exploited as fluorescent probes for macrophages imaging, while micro-patterns with reversible changing of emission color were induced via thermal treatment and direct laser lithography.