Taking into account X-ray diffraction, one of the well-known methods for calculating the stress-strain of crystals is Williamson-Hall (W–H). The W-H method has three models, namely (1) Uniform deformation model (UDM); (2) Uniform stress deformation model (USDM); and (3) Uniform deformation energy density model (UDEDM). The USDM and UDEDM models are directly related to the modulus of elasticity (E). Young’s modulus is a key parameter in engineering design and materials development. Young’s modulus is considered in USDM and UDEDM models, but in all previous studies, researchers used the average values of Young’s modulus or they calculated Young’s modulus only for a sharp peak of an XRD pattern or they extracted Young’s modulus from the literature. Therefore, these values are not representative of all peaks derived from X-ray diffraction; as a result, these values are not estimated with high accuracy. Nevertheless, in the current study, the W-H method is used considering the all diffracted planes of the unit cell and super cells (2 × 2 × 2) of Hydroxyapatite (HA), and a new method with the high accuracy of the W-H method in the USDM model is presented to calculate stress (σ) and strain (ε). The accounting for the planar density of atoms is the novelty of this work. Furthermore, the ultrasonic pulse-echo test is performed for the validation of the novelty assumptions.