Phosphorus (P) is one of the essential macro-elements for plants. Sugar and organic acid are important factors affecting sensory characteristics of citrus fruit quality. The aim of this study was to investigate how P fertilizer affects quality improvement particularly sucrose (Suc), fructose (Fru), glucose (Glu) and citric acid (CA) accumulations in Cara Cara navel. P fertilizer improved fruit quality of Cara Cara navel, as supported by decreasing titratable acid (TA), CA and increasing soluble solid (TSS), sugars and the ratio of TSS and TA. At the early stage of fruit development, P fertilizer had greater roles in degrading Suc into Fru and Glu due to the increased activities of Suc-degrading enzymes including acid invertase, neutral invertase and Suc synthase-cleavage activity. Coversely, at the mid and late stages of fruit development, P fertilizer had greater roles in re-synthesizing Suc due to the increased activities of Suc-synthesizing enzymes including Suc phosphate synthase and Suc synthase-synthetic activity. These results indicated that application of P fertilizer increased soluble sugars concentrations by improving Suc metabolism and sink strength in fruit conferred by the upregulations of the activities of Suc-degrading and Suc-synthesizing enzymes. P fertilizer decreased CA accumulations at least partially by inhibiting synthesis of CA due to the decreased activities of CA-synthesizing enzymes including citrate synthetase and phosphoenolpyruvate carboxylase. This study suggested that P fertilizer, particularly fertilized with 0.40 kg/plant, increased soluble sugars but decreased CA accumulations in citrus fruit.