This paper presents a new modification of the nanostructure of CaSO₄·2H₂O crystals containing nanopores. This nanoporous structure was achieved in phosphogypsum samples that were modified by sodium carbonate and alum. The effects of sodium carbonate and alum on the properties of phosphogypsum were studied. X-ray diffraction (XRD) and scanning electron microscopy (SEM) methods were used to explore the micro-mechanism of the composite system. Subsequently, molecular dynamics simulations were used to study the nanopore structures of the modified CaSO₄·2H₂O. The results show that the addition of sodium carbonate and alum reduced the absolute dry density by 23.1% compared with the original phosphogypsum sample, with a bending strength of 2.1 MPa and compressive strength of 7.5 MPa. In addition, new hydration products, sodium sulfate and sodium aluminum sulfate, were formed in the sample doped with sodium carbonate and alum. A new nanostructure of CaSO₄·2H₂O crystal containing nanopores was formed. Molecular simulations show that the hydration products were responsible for the surface nanopore formation, which was the main factor leading to an increase in mechanical strength. The presented nanopore structure yields lightweight and high strength properties in the modified phosphogypsum.