The porous nature of coral aggregate challenges the manufacturing of high performance coral concrete, which obstacles its development and application. By using microbubble aeration clean technology, this study reports an ecofriendly and economical method to modify coral aggregates. This improvement can overcome the technical bottleneck of manufacturing high performance coral concrete. Innovatively, phosphoric acid (which is also a retarder) was used to clean the original coral aggregate particles, and alkali-activated materials (AAMs) were used to coat coral aggregates. Subsequently, AAMs were used as binder to manufacture the high performance coral concrete. The microbubble aeration cleaning removed loose attachments and soft layer on the surface of coral aggregates. It improved the filling effect of AAM coating into pores and enhanced the interfacial bonding between the aggregate and the AAM coating. The microbubble aeration clean technology modified the interfacial transition zone of coral concrete, successfully solved the problem of poor interface between coral aggregates and mortar. The residual phosphoric acid and phosphate on the aggregates could prolong the setting time of AAM based coral concrete. Comparing to the concrete prepared with original coral aggregates, the concrete prepared using the proposed new method extended initial and final setting times by 34 min and 54 min, improved flexural strength by 32.9% and compressive strength by 35.1%, meeting the performance requirements of the most ocean reef construction requirements.