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This study aims to investigate the influence of adding <i>Lonicera japonica</i> (<i>L. japonica</i>) and <i>Radix Puerariae</i> crude extracts and their mixture to the diet of finishing pigs on their fecal microbes and nutrient apparent digestibility. A total of 72 healthy Duroc × Landrace × Yorkshire crossbred barrows without significant differences in body weight (93 ± 2 kg) were selected and randomly divided into four groups (18 in each group). Three replicate pens per group (six pigs per pen) were used, and two pigs were evaluated for each pen. The groups were fed the following diets: control group (CON), basic diet; chlorogenic acid group (CGA group), basic diet + 1 kg/ton <i>L. japonica</i> crude extract; Pueraria flavonoid group (PF group), basic diet + 1 kg/ton <i>Radix Puerariae</i> crude extract; and mix group (Mix group), basic diet + 0.5 kg/ton <i>L. japonica</i> crude extract + 0.5 kg/ton <i>Radix Puerariae</i> crude extract. The following results were obtained: (1) At the phylum level, Bacteroidetes, Firmicutes, Spirochaetes, Proteobacteria, Fibrobaeteres, and Kiritimatiellaeota were the main components of the fecal microbiota (top 5); the relative abundance of bacteria from phyla Firmicutes significantly increased in the Mix group than in the CON group (<i>p</i> < 0.05). At the genus level, Treponema_2, Rikenellaceae_RC9_gut_group, uncultured_bacterium_f_Lachnospiraceae, uncultured_bacterium_f_Prevotellaceae, and Prevotellaceae_NK3B31_group were the main components of the fecal microbiota (top 5); the relative abundance of bacteria from genus Lactobacillus significantly increased in the Mix group than in the CON group (<i>p</i> < 0.05). Chao1 and Ace counts were significantly higher in group CGA than in the CON group and group Mix (<i>p</i> < 0.05). The alpha and beta diversities and the relative abundance of fecal microbes were higher in all test groups than in the CON group. (2) The protein digestibility was significantly higher in the CGA and PF groups than in the CON group, and the TP digestibility was significantly higher in the CGA than in the CON and Mix groups (<i>p</i> < 0.05). In conclusion, <i>Lonicera japonica</i> and <i>Radix Puerariae</i> crude extract supplementation in the diet significantly changed fecal microbiota and improved the protein and TP digestibility of finishing pigs.