The growing demand for various types of paper highlights the importance of optimizing the kraft pulping process to achieve desired paper properties. This work proposes a novel multiscale model to optimize the kraft pulping process and obtain desired paper properties. The model combines mass and energy balance equations with a layered kinetic Monte Carlo (kMC) algorithm to predict the degradation of wood chips, the depolymerization of cellulose, and the spatio-temporal evolution of the Kappa number and cellulose degree of polymerization (DP). A surrogate LSTM-ANN model is trained on data generated from the multiscale model under different operating conditions, dealing with both time-varying and time-invariant inputs, and an LSTM-ANN-based model predictive controller is designed to achieve desired set-point values of the Kappa number and cellulose DP while considering process constraints. The results show that the LSTM-ANN-based controller is able to drive the process to desired set-point values with the use of a computationally faster surrogate model with high accuracy and low offset.