Phosphorus (P) is an essential macro-element for crop growth and is involved in critical physiological and biochemical processes in plants. Pitaya is an important economic crop in tropical and subtropical regions. High fruit P concentration and huge yield require high P demand for pitaya growth. However, the P absorption characteristics of pitaya and the relationship of root morpho-physiological processes and P uptake are still unclear. In this study, pitaya variety Soft Dahong, which is the most popular cultivar in China, was used. Five P gradients of 0, 0.01, 0.1, 0.5 and 1.0 mmol/L were set by hydroponic experiment to explore the changes of root morphology and physiological process of pitaya under different P application rates. At the same time, the content of phosphorus and other nutrient elements in the aboveground part were analyzed to clarify the mechanism of root morphological and physiological traits for efficient P use and the effect of P supply on other nutrients uptake in pitaya. The results showed that compared with no P, P fertilizer application did not affect the accumulation of aboveground biomass. P uptake and P concentration of shoot increased with the P application rates. The total root length and the number of fine roots with diameter≤0.05 mm in low P treatment (0.1 mmol/L) were significantly higher than those of other treatments. High P supply inhibited root growth, showing that the total root length was the shortest, and the number of coarse roots with diameter≥2 mm was higher than that of other treatments. Low P (0.01 mmol/L) treatment had the highest total organic acid content and higher root CEC content. Compared with no P, the organic acid secretion rate and root CEC content decreased under high P supply (1.0 mmol/L). In terms of the absorption of other nutrient elements, the absorption concentration of iron in the mother branch and the primary branch decreased gradually with the increase of P rate. The contents of nitrogen, calcium, magnesium, manganese and zinc in the second order branches decreased gradually with the increase of P rate, showing a significant negative correlation. This study showed that low P and moderate P supply (0.01 mmol/L or 0.1 mmol/L) could promote root growth, root organic acid secretion and ion absorption capacity of pitaya, while excessive P supply (1.0 mmol/L) significantly inhibited root growth and significantly reduced the absorption of trace elements accumulation in shoots. Therefore, rational application of P fertilizer is of great significance for pitaya to maximize its root biological potential and improve the P use efficiency, and also plays a key role in the balance of trace elements uptake in plants.