In this paper, a novel approximation to the Caputo time fractional derivative of variable order (VO) [Formula: see text] ([Formula: see text]) is established. Since time fractional derivatives are integral, with a weakly singular kernel the discretization on the uniform mesh may not lead to satisfactory accuracy. So, numerical approximation is constructed on nonuniform meshes based on Newton interpolation polynomial. As a result, the novel approximation can be viewed as the modification of the existing method [Shen, S., Liu, F., Chen, J., Turner, I. and Anh, V. [2012] “Numerical techniques for the variable order time fractional diffusion equation,” Appl. Math. Comput. 218(22), 10861–10870]. The truncation errors and some significant properties of coefficients are analyzed. Furthermore, we derived Scheme-I and Scheme-II with second-order accuracy in spatial direction to solve the mobile–immobile advection–dispersion model (MIMADM) based on the VO Caputo derivative. The designed scheme converts the considered problems into a linear system of equations. Moreover, the stability properties of Scheme-I are discussed in detail. Ultimately, the proposed scheme is examined on several text examples demonstrating the high precision and effectiveness of the scheme. Also, comparative study between the outcomes achieved by implementing the suggested scheme with other numerical scheme in the existing literature is provided and also the acquired numerical results of these applications indicate that the suggested technique performs extremely well in terms of reliability and capability.