Filamentous algae, represented by Spirogyra and Cladophora, existed widely in various natural and aquatic waters, and their overgrowth posed a threat to aquatic environment and cultured animals. In order to explore the key factors of filamentous algae occurrence, this paper selected five groups of filamentous algae occurred ponds and no filamentous algae occurred ponds with the same environment and belonging to the same farmers, and analyzed the water quality, bioavailable nitrogen and phosphorus in sediment and detected filamentous algae propagules. The results showed that there were no significant differences in total nitrogen and phosphorus levels between filamentous algae occurred ponds and no filamentous algae occurred ponds in five groups (P > 0.05), whereas the content of Chlorophyll a in filamentous algae occurred ponds in four groups was significantly higher than that in no filamentous algae occurred ponds (P < 0.05). The average bioavailable nitrogen content in the sediment of filamentous algae occurred ponds in the five groups was 15.72 ± 3.60 mg kg-1, whereas the average bioavailable nitrogen content in the sediment of no filamentous algae occurred ponds in the five groups was 13.22 ± 1.97 mg kg-1, 2.50 mg kg-1 lower than that of the former. The average available phosphorus content in the sediment of filamentous algae occurred ponds in the five groups was 72.26 ± 10.57 mg kg-1, and that of no filamentous algae occurred ponds in the five groups was 50.33 ± 12.62 mg kg-1, 21.93 mg kg-1 lower than that of the former. The ratio of available N/P in sediment was below 0.5 in the five groups, and the ratio of available N/P in no filamentous algae occurred ponds was 26.32% higher than filamentous algae occurred ponds. Phytoplankton growth could be inhibited in low N/P ratio condition, whereas filamentous algae has strong adaptability to low nitrogen content and N/P ratio environment, therefore, at the beginning of culturing, the conditions of low nitrogen content and low N/P ratio in the sediment made the phytoplankton in the initial niche competition with filamentous algae at a disadvantage, even if the OTUs number of phytoplankton detected was larger than that of filamentous algae propagules, it did not make it the dominant species under the above conditions. In addition, the detection of filamentous algae propagules showed that they were widely presented in water bodies and sediment of filamentous algae occurred ponds, no filamentous algae occurred ponds and water sources, and filamentous algae propagules were detected even in sterilized and sun-exposed ponds. However, the number of filamentous algae propagants could be reduced by sterilizing and sun-exposing ponds. Therefore, quicklime or bleaching powder alone cannot completely eliminate the occurrence of filamentous algae, but can be used as an auxiliary control measure, and the regulation of bioavailable nitrogen content and the ratio of nitrogen and phosphorus to control the interspecific niche competition is a promising direction of controlling filamentous algae worth further study.