Cyanobacteria are ever-present, mainly flourishing in aquatic environments and surviving virtually in other habitats. The microbiota of indoor dust on the pre-filter of heating, ventilation, and air-conditioning (HVAC) systems, which reflect indoor microbial contamination and affect human health, has attracted attention. Contemporary studies on cyanobacteria deposited on the pre-filter of HVAC remain scant. By the culture-independent approach of qPCR and high throughput sequencing technologies, our results documented that the cyanobacterial concentrations were highest in autumn, occurred recurrently, and were about 2.60 and 10.57-fold higher than those in winter and summer. We proposed that aquatic and terrestrial cyanobacteria contributed to the pre-filter of HVAC by airborne transportation produced by wave breaks, bubble bursts, and soil surface by wind force, owing to the evidence that cyanobacteria were commonly detected in airborne particulate matters. The cyanobacteria community structure was characterized in Shanghai, where Chroococcidiopsaceae, norank_cyanobacteriales, Nostocaceae, Paraspirulinaceae, and others dominated the dust on the pre-filter of HVAC. Some detected genera, including Nodularia sp., Pseudanabaena sp., and Leptolyngbya sp., potentially produced cyanobacterial toxins, which need further studying to determine their potential threat to human health. The present work shed new insight into cyanobacteria distribution in the specific environment besides aquatic habitats.