The variance-based sensitivity analysis methods, nowadays, have found wide-ranging applications in various scientific fields for modelling analysis. The Sobol and EFAST variance-based sensitivity analysis techniques have attracted more attention due to their capabilities. Since the Sobol method has a lower computational efficiency relative to the EFAST, in this paper, the EFAST method is used for the first time for the sensitivity analysis of the parameters of 5 contact nanomechanics models in the AFM-based manipulation of biological cells in bio-environments. The aim of this work is to analysis and compare the sensitivities of theoretical and experimental contact models. In this analysis, the Young’s modulus, adhesion energy, Poisson’s ratio and the particle radius have been considered as the effective parameters. The results indicate that the adhesion energy and the Young’s modulus are the sensitive parameters and the Poisson’s ratio and particle radius are the insensitive parameters.