Despite impressive advancements in various multimodal tasks, vision-language models (VLMs) still struggle with compositional understanding due to limited exposure to training samples that contain subtle variations within paired examples. With advances in multimodal generative models, a natural solution is to generate synthetic samples with subtle variations for training VLMs. However, generating and training on synthetic samples with subtle variations presents two challenges: difficulty in accurately creating precise variations and inconsistency in cross-modal alignment quality. To address these challenges, we propose SVD-GT (Subtle Variation Data Generation and Training), which integrates image feature injection into a text-to-image generative model to enhance the quality of synthetic variations and employs an adaptive margin loss to differentiate samples using adaptive margins, which help filter out potentially incorrect synthetic samples and focus the learning on informative hard samples. Evaluations on four compositional understanding benchmarks demonstrate that SVD-GT significantly improves the compositionality of VLMs, boosting the average accuracy of CLIP by over 8% across all benchmarks and outperforming state-of-the-art methods by 2% on three benchmarks.