Cypress (Cupressus funebris Endl.) is a major tree species planted for forestland restoration in low-fertility soil and in areas where rocky desertification has occurred. Calcium (Ca) fertilizer can adjust the pH of soil and has an important effect on the growth of cypress. Soil and water losses are serious in Southern China, and soil acidification is increasing, which results in high calcium loss. However, the adaptability of cypress clones to different concentrations of calcium in acidic soils has not been studied. In this investigation, a potted-plant experiment was set up with three concentrations of calcium oxide (CaO) fertilizer (0, 3, and 6 g·kg⁻¹) added under local soil conditions with 0 and 3 g·kg⁻¹ nitrogen (N), phosphorus (P), and potassium (K) fertilizer. The effects of CaO on the growth, root development, and nutrient uptake and utilization efficiency of cypress clones were analyzed. The growth, root development, and nutrient absorption and utilization of cypress differed when calcium fertilizer was applied to acidic soils with different degrees of fertility. In the soil with 0 g·kg⁻¹ NPK fertilizer, the 3 and 6 g·kg⁻¹ CaO treatments significantly increased the clonal growth of cypress seedling height, basal diameter, and dry-matter weight. In addition, the length, surface area, and volume of the roots less than 2.0 mm of root diameter also significantly increased, indicating that the fine cypress roots were somewhat able to adapt to differing Ca levels under lower fertility conditions. Moreover, the efficiency of N, P, and Ca accumulation was highest in the 3 g·kg⁻¹ CaO treatment. After adding 3 g·kg⁻¹ CaO fertilizer to the soil with 3 g·kg⁻¹ NPK fertilizer, only the root dry-matter weight increased significantly, indicating that root development (including root length, surface area, and volume) in the D1–D3 diameter classes (≤1.5 mm in diameter) was significantly elevated. When CaO application reached 6 g·kg⁻¹, the seedling height, basal diameter, and dry-matter weight of each organ decreased, as did the length, surface area, and volume of the roots in the all diameter classes, indicating that the addition of excessive CaO to fertile soil could inhibit the growth and root development of cypress. In Ca-deficient low-quality acidic soils, adding CaO fertilizer can promote the development of fine roots and the uptake and utilization of N, P, and Ca. The results of this study provide a basis for determining the optimal fertilization strategy when growing cypress in acidic soils in Southern China.