This study used pepper straw as the fermentation substrate to investigate the effects of different molasses addition levels on the nutritional quality, fermentation quality, and microbial community of pepper straw in micro-storage. A control group (CON) and groups with different molasses addition levels (PA (2.0%), PB (4.0%), PC (6.0%)) were established. The results showed that the addition of molasses effectively reduced the dry matter (DM) loss rate in micro-storage of pepper straw. Compared with the control group, the 4% and 6% treatment groups significantly reduced the dry matter (DM) loss rate. In the 6% treatment group, crude protein (CP) content increased by 1.51 percentage points; at the same time, it significantly increased the relative abundance of Lactobacillus in the fermentation system, lowered the pH, and increased the concentrations of lactic acid (LA) and acetic acid (AA), with the 6% treatment group exhibiting the lowest pH value of 4.18. In summary, the optimal addition range is 4.0–6.0%. Considering production costs, we recommend an addition level of 4.0%.