<p><i>Phaeocystis globosa</i> is one of the major dominant species that cause harmful algae, and its massive reproduction will have a significant impact on marine ecosystems and aquaculture. Therefore, the development of sensitive, fast and portable detection methods is crucial for early identification of algae and follow-up risk assessment. Based on the split aptamer identification strategy, this study constructs a split aptamer-lateral flow dipstick (SA-LFD) platform for the detection of <i>P. globosa</i>, and systematically evaluates its analysis performance. The results show that the method is simple to perform and yields clearly visible results, with the caveat that sample pretreatment requires centrifugation. The system has high specificity for <i>P. globosa</i>, and no cross-reaction was detected in various non-target algae tested. The detection limit of the system is 1.35 × 10³ cells mL^− 1, and it also shows robustness in mixed algae communities and simulated natural seawater samples, indicating that it has a high resistance to matrix interference. The split aptamer strategy effectively reduced background signal interference and improved detection accuracy. Overall, this method integrates sensitivity, specificity, and portability, making it suitable for rapid laboratory-based screening and emergency assessment, and provides a feasible technical approach for the rapid detection of harmful algae and red tide early warning, with potential extension to the detection of other algal species after further simplification of sample pretreatment.</p>