With the increasing shortage of feed resources, hybrid Pennisetum (HE) shows promise as a potential animal feedstuff. The present study aimed to evaluate the fermentation quality, microbial community and functional shifts in HE during ensiling. HE was ensiled naturally (NHE) for 1, 3, 7, 15, 30 and 60 days. After 60 days of ensiling, NHE presented acetate-type fermentation with a high pH value (5.02), as well as acetic acid, butyric acid (0.33% DM), ethanol and ammonia nitrogen (14.0% TN) concentrations, while low lactic acid levels. Enterobacter (45.57%), Klebsiella (12.95%) and Lactococcus (10.24%) were dominant in the 3-day NHE, while Enterobacter (26.27%), Clostridium sensu stricto 11 (21.15%) and Lactobacillus (18.51%) were the most abundant genera in the 60-day NHE. Spearman’s correlation heatmap revealed a positive relationship between Clostridium sensu stricto 1 and ammonia nitrogen, ethanol and butyric acid concentrations. Our analysis of functional profiles obtained from the Kyoto Encyclopedia of Genes and Genomes (KEGG) showed significant differences between fresh and ensiled HE. The ensiling process suppressed amino acid, cofactors, vitamins and energy metabolism, but promoted metabolism associated with carbohydrates and nucleotides. The results of next-generation sequencing in combination with KEGG functional predictions revealed distinct differences in the initial and late phases of ensiling both in terms of community succession and functional shifts. Additional management measures such as delayed harvest or lactic acid bacteria inoculation are necessary to reduce nutrient loss and improve the fermentation quality of NHE.