The high temperatures and dry air environments hinder calcium absorption in tomatoes ( Solanum lycopersicum L.), seriously decreasing tomato yield. Reducing atmospheric vapor pressure deficit (VPD) and increasing calcium fertilizer (Ca) are important measures to improve calcium absorption and distribution in fruits. However, it remains unclear how the changes in tomato fruit morphology and physiology, structural stability, metabolite content, photosynthesis, stomata, and water transport capacity drive calcium absorption under different VPDs and Cas. This study examined the role of fruit morphology and physiology, structural stability, metabolite content, photosynthesis, stomata, and water transport capacity on tomato fruit calcium absorption and distribution under high and low VPDs and Cas. The results showed that reducing VPD and increasing Ca increased the content of calcium pectinate, enhanced the stability of cell wall structure. Meanwhile, reducing VPD and increasing Ca increased carbon dioxide absorption and fixation, but a large amount of fruit carbohydrate content decreased. Additionally, reducing VPD and increasing Ca increased the calcium distribution in fruits by optimizing plant water status, and decreased the calcium distribution in leaves and carpopodium. These results indicate that the stability of cell wall structure, carbon absorption, fixation and accumulation, and water transport capacity effectively regulate plant calcium absorption and distribution under different VPDs and Cas.