Nanoparticles are widely suggested as targeted drug-delivery systems. In photodynamic therapy (PDT), the use of multifunctional nanoparticles as photoactivatable drug carriers is a promising approach for improving treatment efficiency and selectivity. However, the conventional cytotoxicity assays are not well adapted to characterize nanoparticles cytotoxic effects and to discriminate early and late cell responses. In this work, we evaluated a real-time label-free cell analysis system as a tool to investigate in vitro cyto- and photocyto-toxicity of nanoparticles-based photosensitizers compared with classical metabolic assays. To do so, we introduced a dynamic approach based on real-time cell impedance monitoring and a mathematical model-based analysis to characterize the measured dynamic cell response. Analysis of real-time cell responses requires indeed new modeling approaches able to describe suited use of dynamic models. In a first step, a multivariate analysis of variance associated with a canonical analysis of the obtained normalized cell index (NCI) values allowed us to identify different relevant time periods following nanoparticles exposure. After light irradiation, we evidenced discriminant profiles of cell index (CI) kinetics in a concentration- and light dose-dependent manner. In a second step, we proposed a full factorial design of experiments associated with a mixed effect kinetic model of the CI time responses. The estimated model parameters led to a new characterization of the dynamic cell responses such as the magnitude and the time constant of the transient phase in response to the photo-induced dynamic effects. These parameters allowed us to characterize totally the in vitro photodynamic response according to nanoparticle-grafted photosensitizer concentration and light dose. They also let us estimate the strength of the synergic photodynamic effect. This dynamic approach based on statistical modeling furnishes new insights for in vitro characterization of nanoparticles-mediated effects on cell proliferation with or without light irradiation.