Diseases like cancer or diabetes mellitus have complicated pathologies which involve the dynamics of molecular milieu and cellular population. To investigate the pathophysiological microenvironment in this context, many functional probes based on photonic nanomaterials have been developed. The critical parameters include oxygen level, pH value, temperature, calcium ion concentration, ATP level, glucose level, reactive oxygen species, hallmark proteins, and the presence of signaling ligands. These parameters can be time-course sensed and read to reveal the dynamic features of critical molecules in pathology. In this chapter, we will introduce various single and multiphoton fluorescence/phosphorescence nanoprobes for the in vivo quantification of critical molecules. Design to overcome biological barriers and degradation in certain disease contexts will be discussed.