This research utilized Fourier transform infrared (FTIR) spectroscopy to analyze and discuss the molecular structure of pig diets, aiming to provide new insights into the application of fermented feeds in livestock and poultry production. Moreover, the impacts of the fermented diet on growth performance, apparent digestibility, blood biochemical indices, and fecal microorganisms at different stages of pig fattening were also explored. Forty-eight pigs (Duroc × Landrace × Large white three-way hybrid) with a mean body weight of 16.55 ± 3.88 kg were randomly divided into three groups with four replicates per group and four pigs per replicate. The control group was fed a basal diet. The pigs in the fermented diet group (T1) were fed Pediococcus acidilactici (PA), Lactobacillus reuteri (LR), and Bacillus velezensis (BS) (ratio of 1:1:1) at a 6% inoculation dose. The pigs in the cooperative fermentation group (T2) were fed 6% PA, LR, BS, and a 0.2% compound enzyme preparation. The T1 and T2 diets were fermented with 45% water at 33 °C for 48 h. The pre-feeding period lasted 7 days, and the experimental period lasted 84 days. The experimental results showed that the bacterial enzyme cooperation fermentation process significantly increased the contents of crude protein, calcium, and phosphorus in the diet; increased the area of amide Ⅰ region; increased the apparent digestibility of neutral detergent fiber and phosphorus; significantly increased average daily gain; and decreased the feed-to-gain ratio in the late fattening and growth period. During the whole experiment, the serum concentrations of total protein and immunoglobulin A were significantly increased, the serum concentrations of superoxide dismutase and glucose were decreased, and the diversity and richness of fecal microorganisms were increased. These results show that the bacterial enzyme cooperative fermentation diet can improve the apparent digestibility of nutrients and improve overall health by increasing the area of amide Ⅰ region.