Understanding political polarization on social platforms is important as public opinions may become increasingly extreme when they are circulated in homogeneous communities, thus potentially causing damage in the real world. Automatically detecting the political ideology of social media users can help better understand political polarization. However, it is challenging due to the scarcity of ideology labels, complexity of multimodal contents, and cost of time-consuming data collection process. In this study, we adopt a heterogeneous graph neural network to jointly model user characteristics, multimodal post contents as well as user-item relations in a bipartite graph to learn a comprehensive and effective user embedding without requiring ideology labels. We apply our framework to online discussions about economy and public health topics. The learned embeddings are then used to detect political ideology and understand political polarization. Our framework outperforms the unimodal, early/late fusion baselines, and homogeneous GNN frameworks by a margin of at least 9% absolute gain in the area under the receiver operating characteristic on two social media datasets. More importantly, our work does not require a time-consuming data collection process, which allows faster detection and in turn allows the policy makers to conduct analysis and design policies in time to respond to crises. We also show that our framework learns meaningful user embeddings and can help better understand political polarization. Notable differences in user descriptions, topics, images, and levels of retweet/quote activities are observed. Our framework for decoding user-content interaction shows wide applicability in understanding political polarization. Furthermore, it can be extended to user-item bipartite information networks for other applications such as content and product recommendation.