With the degradation of coral reefs induced by climate change and local environmental stressors, an increasing abundance of macroalgae is observed. The sublethal damage caused by macroalgae to corals includes inhibiting growth, development, and reproduction. However, different seaweeds have different effects on different corals, and the effects of macroalgae on corals are still inconclusive. In order to explore the changes in the competitive relationship between corals and macroalgae under thermal stress, Acroproa hyacinthus and Caulerpa taxifolia were selected as the research objects. And two temperatures were established: ambient temperature (27℃) and thermal stress (30℃). Moreover, the effects of water-mediated interaction and direct contact interaction between algae and coral on microbiomes were compared. The reasons affecting microorganisms on the surface of corals were explored from the culture water environment and the surface of macroalgae. The results showed that after removing the chimeras, a total of 3369713 optimised sequences were obtained and most of the bacteria were annotated for subsequent analysis. The microbial expression patterns of water-mediated interaction and direct contact interaction were close to each other at ambient temperature, with species, abundance and PcoA being the highest in both groups. At the phylum level, the main microorganisms were Proteobacteria, Bacteroidota, Cyanobacteria, Firmicutes and Actinobacteriota, etc. in all groups. At the order level, the main microorganisms were Rhodobacterales, Flavobacteriales, Enterobacterales, Cyanobacteriales, Pseudomonadales, Chitinophagales, etc. in all groups. The main phenotypic types of these bacteria were mainly enriched in gram negative, aerobic, contains mobile elements and stress tolerant, while the ecological functions were mainly enriched in chemoheterotrophic and aerobic chemoheterotrophic. A total of 139 core ASVs (amplicon sequence variants) were obtained from 36 samples from 12 treatment groups. The core ASVs were dominated by Pseudomonas, Flavobacteria, Chitinophagales, Rhodobacterales and also included Rickettsiales, Burkholderiales, Enterobacterales, and Verrucomicrobiales. Bacteria that were significantly different in each group were identified using LDA (linear discriminant analysis). At the genus level, the relative abundance of Vibrio, Plesiomonas, Neisseria, and Brevinema significant increased at ambient temperature (LDA > 4, P < 0.05). Coral bleaching occurred after the temperature increased, and the abundance of pathogenic microorganisms, such as Micavibrionales and Rickettsiales significant increased (LDA > 4, P < 0.05). Under thermal stress, co-culture with macroalgae alleviated coral bleaching, reduced the abundance of intracellular parasitic microorganisms, and increased the abundance of Marivita and Halioxenophilus (LDA>4, P < 0.05). Therefore, the C. taxifolia acted as both a stressor to transfer pathogenic bacteria at ambient temperature and assisted the coral to resist intracellular parasitic bacteria at thermal stress. The results help to understand the competition between macroalgae and corals, and explain the potential ecological impact of macroalgae.