<p>Recent advances have enabled the generation of both unpaired (separate profiling) and paired (simultaneous measurement) single-cell multi-modal datasets, driving rapid development of single-cell multi-modal integration tools. Nevertheless, there is a pressing need for a comprehensive benchmark to assess algorithms under varying integrated dataset types, integrated modalities, dataset sizes and data quality. Here we present a systematic benchmark for 40 single-cell multi-modal integration algorithms involving modalities of DNA, RNA, protein and spatial omics for paired, unpaired and mosaic datasets (a mixture of paired and unpaired datasets). We evaluated usability, accuracy and robustness to assist researchers in selecting suitable integration methods tailored to their datasets and applications. Our benchmark provides valuable guidance in the ever-evolving field of single-cell multi-omics.</p>