This study explored the collaborative effect on nutrients removal performance and microbial community in solid-phase denitrification based bacteria-algae symbiosis system. Three biodegradable carriers (apple wood, poplar wood and corncob) and two algae species (Chlorella vulgaris and Chlorella pyrenoidosa) were selected in these bacteria-algae symbiosis systems. Results demonstrated that corncob as the carrier exhibited the highest average removal efficiencies of total nitrogen (83.7%–85.1%) and phosphorus removal (38.1%–49.1%) in comparison with apple wood (65.8%–71.5%, 25.5%–32.7%) and poplar wood (42.5%–49.1%, 14.2%–20.7%), which was mainly attributed to the highest organics availability of corncob. The addition of Chlorella acquired approximately 3%–5% of promotion rates for nitrated removal among three biodegradable carriers, but only corncob reactor acquired significant promotions by 3%–11% for phosphorous removal. Metagenomics sequencing analysis further indicated that Proteobacteria was the largest phylum in all wood reactors (77.1%–93.3%) and corncob reactor without Chlorella (85.8%), while Chlorobi became the most dominant phylum instead of Proteobacteria (20.5%–41.3%) in the corncob with addition of Chlorella vulgaris (54.5%) and Chlorella pyrenoidosa (76.3%). Thus, the higher organics availability stimulated the growth of algae, and promoted the performance of bacteria-algae symbiosis system based biodegradable carriers.