Optical Tweezers (OT), as a revolutionary innovation in laser physics, has been extremely useful in studying cell interaction dynamics at a single-cell level. The reversible aggregation process of red blood cells (RBCs) has an important influence on blood rheological properties, but the underlying mechanism has not been fully understood. The regulating effects of low-level laser irradiation on blood rheological properties have been reported. However, the influence of pulsed laser irradiation, and the origin of laser irradiation effects on the interaction between RBCs remain unclear. In this study, RBC interaction was assessed in detail with OT. The effects of both continuous and pulsed low-level He–Ne laser irradiation on RBC aggregation was investigated within a short irradiation period (up to 300 s). The results indicate stronger intercellular interaction between RBCs in the enforced disaggregation process, and both the cell contact time and the initial contact area between two RBCs showed an impact on the measured disaggregation force. Meanwhile, the RBC aggregation force that was independent to measurement conditions decreased after a short time of pulsed He–Ne laser irradiation. These results provide new insights into the understanding of the RBC interaction mechanism and laser irradiation effects on blood properties.