This paper investigates the effect of carbon nanotube (CNT) deformation on the electrical conductivity of CNT polymer composites at crossed nanotube junctions using a revised 3-dimensional CNT percolating network model. Two aspects of the work are considered. The first is concerned with the effect of CNT deformation on its intrinsic and contact resistances at CNT-CNT junctions. An analytical model based on electron ballistic tunneling theory and Landauer-Büttiker formula is proposed to describe the variation of CNT-CNT contact resistance at the CNT-CNT junction in terms of local deformation of CNT walls and CNT-CNT distance. In addition, a model exclusively based on experimental data to describe the change of CNT intrinsic resistance in terms of its cross-section deformation is adopted. The second is concerned with the relationship among the CNT-CNT distance, the angle between two adjacent CNTs, and the dimensions of local deformation of CNT walls and its impact on the corresponding intrinsic and contact resistance of CNTs near and at a CNT-CNT junction. Finally, Monte Carlo simulations are conducted to evaluate these effects on the electrical conductivity of nanocomposites for different CNT weight fractions. Our results reveal that the local deformation of CNT walls plays a significant role in the evaluation of electrical conductivity of CNT polymer composites. The intrinsic resistance in the deformed part of CNTs near a CNT-CNT junction increases much faster than the decrease of CNT-CNT contact resistance at the same junction when two CNTs are getting closer, resulting in a net increase of resistance at the junction. Numerical results show that the current model agrees with existing experimental data better than existing models without considering the effect of CNT deformation, which tends to overestimate the electrical conductivity of CNT polymer composites containing homogeneously dispersed percolating CNT network.