Phosphorus (P) is one of the most essential mineral elements and macronutrients required for plant growth and development, and its deficiency can affect the physiological and transcriptomic levels of plants, especially in acidic soils. Neolamarckia cadamba (N. cadamba) is a fast-growing tree species widely distributed in tropics and subtropics with acidic soils. However, the physiological and molecular responses of N. cadamba to phosphorus deficiency (PD) have not been well explored. Here, the responses of N. cadamba to PD stress were studied in hydroponic solution. PD stress reduced plant height, leaf size and biomass as well as photosynthetic capacity, but promoted root growth. Stem thickening of secondary xylem and lignification were promoted under PD stress. Meanwhile, the contents of P, Mg and Fe were significantly reduced, while those of Ca and Al were increased. Interestingly, antioxidant enzymes (e.g., POD, MDA, and CAT) were increased by PD stress, especially after 3 weeks. Transcriptome analysis showed that P uptake and transport-related genes PHT, PHO, PT, PAP, SPX, etc. were up-regulated in the root and stem of N. cadamba under PD stress. However, some genes involved in cation transporter and photosystem as well as chlorophyll proteins were down-regulated. Notably, genes associated with the lignin pathway and encoding reactive oxygen species (ROS) enzymes as well as transcription factors (mostly comprising MYB, bZIP, AP2, and HD-ZIP) were mainly up-regulated. Our findings provide new insights into the complex physiological and molecular mechanisms of the PD response in N. cadamba.