Polymeric nanoparticles with a hydrophobic core are valuable biomedical materials with potential applications in in vivo imaging and drug delivery. These materials are effective at protecting vulnerable molecules, enabling them to serve their functions in hydrophilic physiological environments; however, strategies that allow the chemical composition and molecular weight of polymers to be tuned, forming nanoparticles to control the functional molecules, are lacking. In this article, we review strategies for designing core–shell nanoparticles that enable the effective and stable encapsulation of functional molecules for biomedical applications. IR-1061, which changes its optical properties in response to the microenvironment are useful for in vitro screening of the in vivo stability of polymeric nanoparticles. An in vitro screening test can be performed by dispersing IR-1061-encapsulated polymer nanoparticles in water, saline, buffer solution, aqueous protein solution, etc., and measuring the absorption spectral changes. Through the screening, the effects of the polarity, molecular weight, and the chiral structure of polymers consisting of polymer nanoparticles on their stability have been revealed. Based on the findings presented here, more methodologies for the effective application of various biomolecules and macromolecules with complex high-dimensional structures are expected to be developed.