Background Acceleration of MR imaging (MRI) is a popular research area, and usage of deep learning for acceleration has become highly widespread in the MR community. Joint acceleration of multiple-acquisition MRI was proven to be effective over a single-acquisition approach. Also, optimization in the sampling pattern demonstrated its advantage over conventional undersampling pattern. However, optimizing the sampling patterns for joint acceleration of multiple-acquisition MRI has not been investigated well. Purpose To develop a model-based deep learning scheme to optimize sampling patterns for a joint acceleration of multi-contrast MRI. Methods The proposed scheme combines sampling pattern optimization and multi-contrast MRI reconstruction. It was extended from the physics-guided method of the joint model-based deep learning (J-MoDL) scheme to optimize the separate sampling pattern for each of multiple contrasts simultaneously for their joint reconstruction. Tests were performed with three contrasts of T2-weighted, FLAIR, and T1-weighted images. The proposed multi-contrast method was compared to (i) single-contrast method with sampling optimization (baseline J-MoDL), (ii) multi-contrast method without sampling optimization, and (iii) multi-contrast method with single common sampling optimization for all contrasts. The optimized sampling patterns were analyzed for sampling location overlap across contrasts. The scheme was also tested in a data-driven scenario, where the inversion between input and label was learned from the under-sampled data directly and tested on knee datasets for generalization test. Results The proposed scheme demonstrated a quantitative and qualitative advantage over the single-contrast scheme with sampling pattern optimization and the multi-contrast scheme without sampling pattern optimization. Optimizing the separate sampling pattern for each of the multi-contrasts was superior to optimizing only one common sampling pattern for all contrasts. The proposed scheme showed less overlap in sampling locations than the single-contrast scheme. The main hypothesis was also held in the data-driven situation as well. The brain-trained model worked well on the knee images, demonstrating its generalizability. Conclusion Our study introduced an effective scheme that combines the sampling optimization and the multi-contrast acceleration. The seamless combination resulted in superior performance over the other existing methods.