In order to effectively use locally available woody forage and hay resources in tropics, paper mulberry (PM) silages were prepared using Napier grass (NG) and rice straw (RS) hays. The mixing proportion of hays were 10%, 20%, and 30% on fresh matter basis. After 60 days of ensiling, single molecule, real-time (SMRT) sequencing technology was used to analyse the dynamic changes of microbial community and silage fermentation. When PM silages were prepared with both hays, the moisture of PM were adjusted below 67.6%. The dominant microbial community rapidly shifted from Gram-negative to Gram-positive bacteria during ensiling. Before ensiling, aerobic bacteria were dominant in materials, but after ensiling, Lactobacillus plantarum became the main bacterial community and dominated the fermentation process. The result of Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis shown that hay-treated PM silages increased the proportion of Global and overview maps and carbohydrate metabolic pathways, while decreasing the proportion of amino acid metabolic pathway. Fatty acid metabolism, glycolysis and proteolysis categories may improve the flavour and quality of the silage. PM silage prepared with 10% hay effectively improved better fermentation quality than PM alone silage. The result confirmed that PM and hay are the ideal combination, they can prepare good-quality silage for ruminant feed to alleviate the shortage of feed in tropics. •Napier grass and rice straw improve fermentation suitability of paper mulberry.•Paper mulberry with 10% hay are the ideal combination for silage preparation.•Microbial metabolic pathways improve the flavour and quality of the silage.•Hay addition increases the proportion of carbohydrate metabolic pathway in silage.•SMRT technology accurately revealed specific microbial information of silage.