The modified teeth are deliberately manufactured to mitigate the stress concentration generated by offset components, which makes equipment more susceptible to localized failures. Therefore, this paper presents a model aimed at investigating the meshing characteristic of gear pair with modification and crack failure. In this model, the tooth deformation and force transmission are determined based on slice coupling theory. The torsional deformation of teeth produced by eccentric load distribution is considered and complemented to the calculation method. Finally, the approach is proven through the experimental tests and FE model. The result shows that when the equipment is operated in misalignment condition, eccentric load distribution, and stress concentration at tooth edge are generated, the meshing stiffness will be reduced drastically, which can be suppressed by appropriate modification, and the rapid decline of meshing stiffness is weakened by increasing the effective contact length. Although the contact stiffness would be further reduced by the crack failure and the tooth surface deformation is increased, it seems to alleviate the stress concentration and eccentric load effectively.