Broussonetia papyrifera L. (paper mulberry) is an alternative woody plant, which can used to replace part of the protein feed for ruminants. Ensiling is an effective way to preserve fresh pasture and to solve the problem of stable storage and feed conversion of paper mulberry in the rapid growth period. However, low dry matter (DM), water-soluble carbohydrate, and lactic acid bacteria (LAB) reduce the quality of paper mulberry silage. This study assesses the influence of wilting time (0 h and 3.5 h; lighting: 3.43 × 104 Lux) and three additives (Enterococcus durans, CL; cellulase, CE; and formic acid, FA) on the fermentation quality, aerobic stability, and bacterial community of whole plant B. papyrifera silage. The whole plant B. papyrifera sample was mowed and wilted for 0 h and 3.5 h, and then had CL, CE, or FA added, followed by 60 days of ensiling. The results show all silage samples had high fermentation quality with pH below 4.2, ammonia-nitrogen below 100 g/kg DM, and no detectable butyric acid. The additives protected the DM and the crude protein from protease activity (p < 0.05), and CL was the most effective among them. Furthermore, wilting time influenced the silage’s bacterial communities, but overall, CL treatment had the greatest impact on bacterial communities. Wilting time and formic acid treatment significantly improved aerobic stability (p < 0.05). Enterococcus was positively correlated with lactic acid (LA), while negatively correlated with LA and Weissella (p < 0.001). Enterococcus was identified as the main driver of the whole plant paper mulberry ensiling process in the present study. In conclusion, compared to other additives, LAB is the most effective and economical to improve the fermentation quality and reduce the protein degradation of whole plant paper mulberry silage. Our findings provide a theoretical basis to improve the quality and production of paper mulberry silage.