Homologous recombination deficiency (HRD) is a well-recognized important biomarker in determining the clinical benefits of platinum-based chemotherapy and PARP inhibitor therapy for patients diagnosed with gynecologic cancers. Accurate prediction of HRD phenotype remains challenging. Here, we proposed a novel Multi-Omics integrative Deep-learning framework named MODeepHRD for detecting HRD-positive phenotype. MODeepHRD utilizes a convolutional attention autoencoder that effectively leverages omics-specific and cross-omics complementary knowledge learning. We trained MODeepHRD on 351 ovarian cancer (OV) patients using transcriptomic, DNA methylation and mutation data, and validated it in 2133 OV samples of 22 datasets. The predicted HRD-positive tumors were significantly associated with improved survival (HR = 0.68; 95% CI, 0.60-0.77; log-rank p < 0.001 for meta-cohort; HR = 0.5; 95% CI, 0.29-0.86; log-rank p = 0.01 for ICGC-OV cohort) and higher response to platinum-based chemotherapy compared to predicted HRD-negative tumors. The translational potential of MODeepHRDs was further validated in multicenter breast and endometrial cancer cohorts. Furthermore, MODeepHRD outperforms conventional machine-learning methods and other similar task approaches. In conclusion, our study demonstrates the promising value of deep learning as a solution for HRD testing in the clinical setting. MODeepHRD holds potential clinical applicability in guiding patient risk stratification and therapeutic decisions, providing valuable insights for precision oncology and personalized treatment strategies.