Synthetic MRI enables reconstruction of multiple MRI contrasts from a single (multi-echo) scan which significantly improves scanning efficiency. However, the existing state-of-the-art voxel-wise model-fitting method is not optimal. The model-fitting method often results in inaccurate parameter estimation and undesired artifacts, especially for T2-FLAIR synthesis as shown in clinical studies. Here a deep learning method is proposed to improve the contrast synthesis from multi-delay multi-echo MR imaging. With T2-FLAIR synthesis as an example, the proposed method outperforms existing model-fitting based method to overcome artifacts and improve synthesis accuracy. The proposed method is an essential component for delivering reliable and accurate synthetic MRI, further accelerating scanning and improving quantitative parameter mapping.