Structural alteration of serum albumin, the major extracellular multifunctional protein in mammals, has been linked to a number of diseases. Herein we present a method based on fluorescence lifetime analysis of near-infrared (NIR) probes bound to albumin to interrogate its structural state without prior isolation of the protein. Molecular modeling study revealed that albumin binds polymethine dyes via two binding sites with different sizes and polarities. As a result, a NIR molecular probe typically exhibits two distinct lifetimes with corresponding fractional contributions. The distribution of fractional contributions along with individual fluorescence lifetimes represents unique parameters for characterizing albumin architecture. To evaluate the effect of size and polarity of binding sites on fluorescence lifetime we studied NIR probes in solutions with different viscosity and polarity. We established that viscosity has negligible effect on polymethine dyes lifetime while the change in polarity has a profound impact. We also established a correlation between fluorescence lifetime and solvent polarity function for a number of NIR dyes for quantitative description of binding sites polarity. After screening a library of dyes, we identified a probe with optimal fluorescence lifetime properties to assess structure-related differences of albumins. The results show that changes in the lifetime of NIR dyes reflect the perturbation of albumin's tertiary structures. Because of the reduced absorption of light by blood in the NIR region, the method developed can be used to determine structural changes of albumins in whole blood.