The enzyme xylanase is more and more widely used in feed production, but different xylanase have different properties, mechanism and application effects. To provide a theoretical basis for choosing more suitable xylanase in feed production, we selected bacterial xylanase (BX), labeled enzyme A, and trichoderma xylanase (TX), labeled enzyme B, and studied the enzymology properties and application effects on growth performance and gut flora in weaned piglets. The results showed that the activity levels of both appear parabolic along with increasing pH or temperature, but the amplitude of enzyme activity changing curves and the pH/temperature of optimal activity level are different, where enzyme A has the optimal activity level at 50 °C with a pH value of 5.0. The optimal activity level of enzyme B was achieved at 70 °C with a pH around 6.0. Enzyme B suffered very little activity loss with moisture level at 16% and temperature from 80 °C to 90 °C. Enzyme A suffered a big drop in activity level when processed with high temperature from around 80 °C to 90 °C, and it was even completely inactivated at 90 °C. Enzyme A has very low activity level after being processed in acid environment, but enzyme B has minor changes in activity level with respect to changes in acid level, indicating significantly different enzymatic properties between the two different sources of xylanases. In feeding experiment, the control group, was fed the basal diet, and the BX group and TX group were fed basal diets supplemented with 0.01% bacterial and fungal xylanases, respectively. The results showed that ADG of the BX group and TX group increased by 3.25% (P > 0.05) and 8.22% (P < 0.05), respectively, and the feed conversion ratio decreased by 6.74% and 7.86% (P > 0.05), respectively compared with the control group; TX group had significantly higher (P < 0.05) ADG compared with BX group; BX group and TX group had significantly lower ileum Escherichia coli level than the control group, which were reduced by up to 12.98% (P < 0.05) and 11.68% (P < 0.05), respectively, but the ileal lactic acid bacteria levels were significantly increased by 16.21% (P < 0.01) and 27.02% (P < 0.01), respectively. There were no significant differences (P > 0.05) between BX group and TX group in terms of lactic acid bacteria E. coli level. We concluded that fungal xylanase (enzyme B) has better performances in improving weaned piglet growth and in increasing ileal lactic acid bacteria level compared with bacterial xylanase (enzyme A).