Continuous cropping obstacles (CCOs) severely restrict the sustainable development of the ginger industry, yet the response mechanisms of rhizosphere microbiome and metabolome to microbial fertilizer under different continuous cropping durations remain unclear. Here, a field experiment was conducted in ginger fields with 5-year (short-term) and 20-year (long-term) continuous cropping history under conventional chemical fertilization, with or without additional microbial fertilizer application. Rhizosphere soil samples were analyzed via metagenomic sequencing and UPLC–MS/MS. Long-term continuous cropping caused severe soil acidification (pH 5.18–5.26 vs. 6.82–6.98 in short-term) and pathogen enrichment. Microbial fertilizer reduced the disease index by 43.47% under long-term cropping and by 31.48% under short-term cropping. It also improved soil properties and enzyme activities (e.g., urease activity increased nearly 12-fold), enriched beneficial genera (Pedobacter, Flavobacterium, Pseudomonas), activated arginine and proline metabolism, and promoted 4-guanidinobutanoic acid accumulation, forming a positive feedback loop with beneficial microbes. In conclusion, microbial fertilizer alleviates ginger CCOs by reshaping the rhizosphere microbiome and metabolome in a continuous cropping duration-dependent manner.