AbstractInteractions between host and bacterial cells are integral to human physiology. The complexity of host–microbe interactions extends to different cell types, spatial aspects, and phenotypic heterogeneity, requiring high‐resolution approaches to capture their full complexity. The latest breakthroughs in single‐cell RNA sequencing (scRNA‐seq) have opened up a new era of studies in host–pathogen interactions. Here, we first report a high‐throughput cross‐species dual scRNA‐seq technology by using random primers to simultaneously capture both eukaryotic and bacterial RNAs (scRandom‐seq). Using reference cells, scRandom‐seq can detect individual eukaryotic and bacterial cells with high throughput and high specificity. Acinetobacter baumannii (A.b) is a highly opportunistic and nosocomial pathogen that displays resistance to many antibiotics, posing a significant threat to human health, calling for discoveries and treatment. In the A.b infection model, scRandom‐seq witnessed polarization of THP‐1 derived‐macrophages and the intracellular A.b‐induced ferroptosis‐stress in host cells. The inhibition of ferroptosis by Ferrostatin‐1 (Fer‐1) resulted in the improvement of cell vitality and resistance to A.b infection, indicating the potential to resist related infections. scRandom‐seq provides a high‐throughput cross‐species dual single‐cell RNA profiling tool that will facilitate future discoveries in unraveling the complex interactions of host–microbe interactions in infection systems and tumor micro‐environments.