This study explored effects of microbial preparation (MIP, developed by our research team) on production performance and body health of Boer goat to reveal the function of it in goat breeding industry. Compound yeast and enzyme preparation (CYP) was used to compare the function of MIP. Healthy male Boer goats (n = 15, BW = 25.31±4.06 kg) were allocated randomly into three groups as NC (Basal diet), MI (Basal diet + MIP) and CY (Basal diet + CYP). This study lasted for 71 days including 15 days for adaptation and 56 days for growth trial. Both MIP and CYP enhanced production performance such as average daily gain of goats, MIP enhanced the level of fat synthesis such as total cholesterol level significantly on day 28. As for rumen fermentation and microbial communities of goat, MIP decreased rumen pH. PCoA analysis showed that the rumen bacterial community on day 28 was significantly separated. In conclusion, MIP increased production performance, ameliorating rumen fermentation and shifting microflora. Our findings provide the evidence for the influence of probiotics on goat production performance as well as health condition.