Trivalent iron ions (Fe(III)) have important effects on aquatic ecosystems, especially on the functional diversity and stability of microorganisms and ecosystems. Here, a cultivable microalgae (Chlorococcum sp. GD) from the natural environment (Shanxi, China) were isolated and identified. A combined high-throughput 16S rRNA gene amplicon sequencing/excitation-emission matrix coupled with parallel factor (EEM-PARAFAC) analysis was used to integrated the results of Fe(III) influence on Chlorococcum sp. GD bacterial community and dissolved organic matter (DOM) characteristics through laboratory experiments. Due to the addition of Fe(III) in the form of ferric nitrate (Fe(NO3)3·9H2O), complexed with EDTA to maintain solubility and bioavailability, the bacterial community was altered. This led to a decrease in the relative abundance of Proteobacteria and Actinobacteria and an increase in the relative abundance of Cyanobacteria, especially under excessive Fe(III) treatment. In addition, the relative contribution of bacterial community dispersal limitation and homogenizing dispersal was 100 %, which may lead to differences in their local adaptation and ecological processes with homogenization of bacterial diversity and loss of function. Excessive Fe(III) caused a significant increase in the abundance of genes involved in the carbon cycle (p < 0.01) and a significant decrease in genes involved in the nitrogen cycle (p < 0.01), further affecting the overall regulatory network of gene expression. This led to an increase in the abundance of genes involved in metabolism, cellular processes, environmental information processing, genetic information processing, and human diseases. The moderate amount of Fe(III) promoted the production of microbial components and accelerated the degree of DOM humification. It is also worth mentioning that excessive Fe(III) inhibited DOM degradation. Overall, this work explored the characteristics of bacterial community and DOM changes in Fe(III)-stressed Chlorococcum sp. GD as an example, which contributes to an in-depth understanding of microbial community diversity and element cycling in aquatic ecosystems.