To explore the mechanism of earthworm compost and biochar on the watermelon-white clover ecosystem, greenhouse experiments were conducted with eight treatments comprising a blank control (watermelon plants), biochar, white clover cover, earthworm compost, white clover cover + earthworm compost, biochar + earthworm compost, white clover cover + biochar, and white clover cover + biochar + earthworm compost. Soil nutrients, microbial community structure, and watermelon metabolomics were analyzed to determine the effects of earthworm compost and biochar on the watermelon-white clover ecosystem. The results indicated that: (1) In the combined treatment, soil bulk density decreased, soil fertility improved, and the absorption capacity of nitrogen, phosphorus, and potassium in watermelon plants increased. The treatment of white clover cover + biochar + earthworm compost (WBV) demonstrated the best overall performance. (2) The richness of microbial communities decreased in the WBV treatment. The Shannon index and Chao 1 index were ranked as BV > WB > CK > WV > WBV treatment. Compared with the control, the relative abundance of Actinobacteria, Proteobacteria, Firmicutes bacteria, and Mortierellomycota fungi in soil microbial communities in the WBV treatment increased significantly, while the relative abundance of Chloroflexi, Acidobacteria, and Verrucomicrobia decreased. (3) Lipid compounds such as alpha-linolenic acid, Lyso-Phosphatidylcholine(17:0), and Phosphatidylinositol Acid(18:1(11Z)/0:0), as well as amino acids such as alanine, aspartate, and glutamate were detected in the watermelon fruit in the WBV treatment. The study found that the combination of white clover cover, biochar, and earthworm compost significantly improved soil nutrient contents of available nitrogen, available phosphorus, and available potassium, promoted the absorption of nitrogen and phosphorus by watermelon, improved the soil microbial environment, altered watermelon plant lipid, organic acid, and amino acid metabolism, enhanced the protection of the watermelon plant biofilm, regulated cell osmosis, and increased stress resistance.