The widespread occurrence of nano-plastics (NPs) in aquatic environments poses emerging challenges to the pollutant removal performance and ecological stability of constructed wetlands (CWs). This study investigates the performance of calcium-modified (Ca-MBF) and manganese-modified basalt fiber (Mn-MBF) bio-nests as novel substrates to mitigate NP-induced inhibition of CWs. Laboratory-scale CWs were operated for 180 days to evaluate substrate-associated enzyme activities, microbial community structure, and functional gene profiles. Results showed that Mn-MBF bio-nests enhanced the activities of dehydrogenase (DHA), urease (UR), ammonia monooxygenase (AMO), nitrite oxidoreductase (NOR), nitrate reductase (NAR), nitrite reductase (NIR), and phosphatase (PST) by 86.2%, 65.5%, 127.0%, 62.8%, 131.5%, 65.3%, and 107.0%, respectively, compared with the control. In contrast, Ca-MBF bio-nests increased these enzyme activities by 48.6%, 53.5%, 67.0%, 30.6%, 95.0%, 45.3%, and 54.6%, respectively. MBF bio-nests also enhanced microbial diversity, enriched denitrifying and phosphorus-removing bacteria (e.g., Thauera, Plasticicumulans), and promoted extracellular polymeric substance secretion. Functional gene prediction indicated elevated abundances of nitrogen cycle-related genes, thereby enhancing nitrification, denitrification, and phosphorus removal processes. These synergistic effects collectively improved nitrification, denitrification, and phosphorus removal efficiency, with Mn-MBF showing superior performance. This study highlights MBF bio-nests as a sustainable strategy to enhance the resilience and long-term operational stability of CWs in environments impacted by nano-plastic pollution.