Gromov-Wasserstein distance has many applications in machine learning due to its ability to compare measures across metric spaces and its invariance to isometric transformations. However, in certain applications, this invariant property can be too flexible, thus undesirable. Moreover, the Gromov-Wasserstein distance solely considers pairwise sample similarities in input datasets, disregarding the raw feature representations. We propose a new optimal transport formulation, called Augmented Gromov-Wasserstein (AGW), that allows for some control over the level of rigidity to transformations. It also incorporates feature alignments, enabling us to better leverage prior knowledge on the input data for improved performance. We first present theoretical insights into the proposed method. We then demonstrate its usefulness for single-cell multi-omic alignment tasks and heterogeneous domain adaptation in machine learning.