A two-year trial was conducted to test the interactive effects of special-for-apple organic fertilizer, CaSO4, and amino acid Ca on Fuji/Balenghaitang (Malus robusta Rehd.) rootstock in Burozem soil in China. Total Ca, exchangeable Ca, and fruit Ca were significantly improved by the soil application of CaSO4 with the highest exchangeable Ca and fruit Ca observed in Fuji apple trees treated at the rate of 3.5 kg CaSO4 per tree. 3.5 kg CaSO4 was divided into two applications, with first application in the first month after full bloom, and the second in the second month after full bloom in summer, progressively to improve fruit Ca concentration. Dividing CaSO4 into two applications in combination with organic fertilizer or amino acid Ca spray, proved to be more effective on improving the fruit Ca concentration, with the highest level of 179.17 mg/kg FW in Fuji apple trees treated with 2 kg CaSO4 applied and amino acid Ca sprayed in the first month after full bloom, 1.5 kg CaSO4 applied in summer, organic fertilizer applied in winter. Organic fertilizer applied in winter alone remarkably improved the fruit Ca concentration, as well as storage Ca in roots and stems, and the best effect was observed in Fuji apple trees which were supplemented organic fertilizer (10 kg) in winter and CaSO4 (1 kg) in the first month after full bloom per tree. The effect on Ca increment became less pronounced when the amount of organic fertilizer reached 15 kg or CaSO4 was more than 3.5 kg per tree. There was a positive correlation between the Ca/Mg ratio in soil and fruit, exchangeable Ca, and fruit Ca concentration, while a negative correlation was observed between the N/Ca ratio in fruit, available P, available K in soil, and fruit Ca concentration. Both N/Ca ratio and Ca/Mg ratio in fruit were affected by different fertilization regime, and bitter pit incidence at the end of storage kept acceptable only if N/Ca<17 and Ca/Mg≥7 at harvest. The commercial fertilization regime turned out to be organic fertilizer in combination with CaSO4 applied in soil in winter, amino acid Ca sprayed in the first month after full bloom, and CaSO4 applied in soil in summer.