Calf diarrhea causes huge economic losses to livestock due to its high incidence and mortality rates. Alkaline mineral complex water is an alkaline solution containing silicon, sodium, potassium, zinc, and germanium, and has biological benefits and therapeutic effects. This study aimed to evaluate the impact of alkaline mineral complex water supplementation on the health of calves and to investigate the effect of Alkaline mineral complex water supplementation on neonatal calf serum variables and the liver transcriptome. Sixty Holstein calves (age 1.88 ± 0.85 days, weight 36.63 ± 3.34 kg) were selected and randomly divided into two groups: the T group (treatment group with alkaline mineral complex water supplemented during the experiment) and C group (control group without alkaline mineral complex water supplementation). Alkaline mineral complex water supplementation significantly increased the body weight for calves aged 60 d and average daily gain during the experimental period (1–60 d). In addition, Alkaline mineral complex water supplementation could significantly decrease the diarrhea rate for calves aged 16–30 d, enhance the T-AOC, IgG, IGF-1, and IGFBP-2 in concentrations. The results of KEGG enrichment analysis in transcriptomics indicate that Alkaline mineral complex water supplementation inhibited the target IL-1B gene of the NF-kappa B signaling pathway of liver. Alkaline mineral complex water supplementation decreased calf diarrhea and improved partial immune function, anti-inflammatory activity, antioxidant capacity, and health of calves. Alkaline mineral complex is a candidate to replace medicated feed additives. Alkaline mineral complex waterAlkaline mineral complex waterAlkaline mineral complex waterAlkaline mineral complex waterAlkaline mineral complex waterAlkaline mineral complex waterAlkaline mineral complex water.