We propose a novel methodology to estimate parameters characterizing a weakly nonlinear Duffing oscillator represented by an optically levitating nanoparticle. The method is based on averaging recorded trajectories with defined initial positions in the phase space of nanoparticle position and momentum and allows us to study the transient dynamics of the nonlinear system. This technique provides us with the parameters of a levitated nanoparticle such as eigenfrequency, damping, coefficient of nonlinearity and effective temperature directly from the recorded transient particle motion without any need for external driving or modification of an experimental system. Comparison of this innovative approach with a commonly used method based on fitting the power spectrum density profile shows that the proposed complementary method is applicable even at lower pressures where the nonlinearity starts to play a significant role and thus the power spectrum density method predicts steady state parameters. The technique is applicable also at low temperatures and extendable to recent quantum experiments. The proposed method is applied on experimental data and its validity for one-dimensional and three-dimensional motion of a levitated nanoparticle is verified by extensive numerical simulations.