Different sampling apparatus have been proposed to withdraw particles from combustion systems. All of them induce perturbations, mostly on the temperature and the velocity field inside the flame. Generally, to avoid artifacts due to velocity field perturbation, the sampling system is set up to obtain isokinetic probing of the combustion products, and the sample reactivity is rapidly frozen by means of water cooling or inert gas dilution. The higher the difference between the combustion temperature and the probe, the higher the perturbation of the probe to the combustion reactions. Since the cooling down of the sampling system is necessary to quench the reactivity of the collected samples, it is not possible to completely avoid temperature perturbation on the flame. A change of the temperature for effect of the probe might influence not only the reactivity of the system but the chemical and morphological properties of the collected particles. In the present work, a detailed kinetic model for particle formation in the flame is used to predict the effect of temperature perturbation induced by the sampling probe on the chemical characteristics and morphology of the particles formed in a rich premixed ethylene flame. Experimental temperature profiles of pristine and perturbed flames available in the literature are used as input to the model. Measured particle size distribution functions are instead used to evaluate model capability to predict particulate formation. Model results show that the cooling down of the flame locally enhances the coagulation process leading to formation of particles with sizes larger than those formed in the unperturbed flame and with more hydrogenated structures. A sensitivity analysis has shown that the decrease of the temperature locally inhibits chemical growth pathways and enhances physical interactions. In particular, both condensation of polycyclic aromatic hydrocarbons (PAHs) and coagulation rate increase by orders of magnitude becoming the predominant pathways for particle formation and strongly affecting the chemical nature of the produced particles.