Single-cell mosaic integration has revolutionized our understanding of cellular heterogeneity, offering unprecedented resolution into cellular states and contexts. While large language models (LLMs) have achieved success in the analysis of single-cell omics data, their application specifically focused on the integration of mosaic data remains limited. Current computational approaches often fall short in addressing these challenges. They frequently depend on assumptions of data completeness and uniform quality, failing to manage the variability and noise effectively introduced by missing data. Moreover, these models might not efficiently process large, diverse datasets or account for biological heterogeneity and long-ranging dependencies across various data types. To address these shortcomings, we introduce the Single-cell Mosaic Omics Nonlinear Integration and Clustering Analysis (scMonica) framework, which employs a LSTM-transformer hybrid architecture. This innovative model combines the strengths of Long Short-Term Memory (LSTM) networks, which excel at capturing long-range dependencies within sequential gene expression patterns, with transformers, renowned for their attention mechanisms that handle the complex, non-linear interactions characteristic of multi-layered datasets. By leveraging these complementary strengths, our approach enhances the integration process significantly, allowing for nuanced management of the intrinsic heterogeneity and sparsity of mosaic datasets. Comprehensive evaluations demonstrate the robustness and effectiveness of our approach, offering unparalleled versatility and accuracy in multi-omics data analysis. These advancements underscore scMonica’s potential to drive significant insights in single-cell developmental biology, oncology, and beyond. We discuss the underlying technologies, analyze their applications, and contemplate future directions that promise to extend the boundaries of both research and clinical domains.