Pinus elliottii × P. caribaea is a widely planted commercial tree hybrid in South China. To investigate the potential of physiological parameters for clonal selection, cuttings of three clones (EH3, EH4 and EH5) and a control were grown in phosphorus treated pots. Significant variations to phosphorous, photosystem II activity and polar metabolite abundance in needles were noted among clones. Clone EH5 was the most P-responsive and had maximum height growth. The highest maximum quantum yield of PSII in the dark (Fv/Fm), maximum quantum yield of PSII in the light (Fvʹ/Fmʹ) and the actual PSII efficiency (ΦPSII) values were also found in EH5. A total of 64 polar metabolites were identified, 21 were regulated by phosphorous, while 28 accumulated differentially among the three clones. There were few overlapping responsive metabolites to phosphorous fertilization. In EH5, the abundance of maltotriitol, neohesperidin and raffinose were highest, whereas galactinol and shikimic acid were lower compared with EH3 and EH4. The results reveal that physiological traits were genetically controlled and might be useful for selecting clones with high phosphorous utilization efficiency.