Simple Summary: In order to find antibiotic substitutes for weaned piglet health and growth, compound probiotics and berberine (CPB) were selected in this study. The results indicated that CPB could replace antibiotics to improve piglet health and decrease mortality, diarrhea and rejection rates. CPB was also able to regulate fecal microbiota as well as improve protein digestibility and serum biochemical parameters. Therefore, CPB might be a good antibiotic alternative in piglet production performance.Abstract: This study was conducted to investigate the effects of dietary supplementation with compound probiotics and berberine (CPB) on growth performance, nutrient digestibility and fecal microflora in weaned piglets. A total of 200 piglets 35 days old were randomly allocated to 5 groups, 4 replications in each group, and 10 piglets in each replication. Group A was the basal diet; group B was supplemented with antibiotics and zinc oxide; groups C, D and E were supplemented with 0.06%, 0.12% and 0.18% CPB, respectively. The experimental period was 42 d. The results indicated that there were no significant differences in average daily feed intake (ADFI), average daily gain (ADG) and feed conversion rate (FCR) among five groups (p > 0.05). However, mortality, diarrhea and rejection rates in the control group were higher than that in other groups. CPB could increase protein digestibility and serum IgG content (p < 0.05), while it could decrease serum urea nitrogen content and alkaline phosphatase activity (p < 0.05). Analysis of fecal microbiota showed that the relative abundances of Bacteroides and Firmicutes were increased, while the relative abundances of opportunistic pathogens such as Spirochaetae and Protebactreria were dramatically decreased in piglets fed with CPB or antibiotics, compared with the control group. Furthermore, CPB intervention increased the relative abundances of Prevotella_9, Megasphaera and Prevotella_2, while decreased the relative abundance of Prevotellaceae_NK3B31_group. Correlation analysis revealed that there was good correlation between serum indexes and fecal microbiota. It was suggested that CPB might be a promising antibiotic alternative for improving piglet health and immunity, decreasing mortality by positively altering gut microbiota.