This study was performed to investigate the influence of 8 strains of probiotics with clear origin and probiotic properties on the metabolite profile of Lactobacillus beverage with different substrates （skim milk powder， soybean protein isolate and whey albumen powder）. The volatiles were identified and quantified by solid-phase microextraction and gas chromatography-mass spectrometry （SPME-GC-MS） and the key volatile flavor compounds were identified via odor active values（OAV） analysis. In total， 107 volatile flavor compounds， consisting of 21 aldehydes， 17 ketones， 13 acids， 23 alcohols， 5 esters， 17 hydrocarbon， 7 nitrogenous compounds， 4 other compounds were identified. The result showed that after the fermentation of complex probiotics， the metabolite profiles were significantly different between Lactobacillus beverage with different substrates. However， there was no significant difference in metabolite profile of Lactobacillus beverage with the same substrate during different storage timepoints. The principal component analysis（PCA） of the key volatile compounds （OAV≥0.1） indicated that for Lactobacillus beverage with skim milk powder， 10 volatiles were identified as the important aroma contributors， such as acetoin， butanal， 3-hydroxy-， 2-nonanone， 2-undecanone； Lactobacillus beverage with soybean protein isolate had 5 key volatiles， such as acetaldehyde， butanal， 3-methyl-， 2-nonen-1-ol. Surprisingly， the contents of hexanal， 1-hexanol and benzaldehyde that cause unpleasant beany flavor were significantly decreased （P<0.05） after fermentation with complex probiotics. Lactobacillus beverage with whey albumen powder also had 6 key volatiles， such as valeraldehyde， 1-heptanol.