A numerical method for high altitude aerothermodynamic analysis code for Very Low Earth Orbit (VLEO) satellite and spacecraft, named as HACS, is presented in this article. HACS is a computational tool that addresses the challenges by integrating the free-molecular gas kinetic model with novel particle sampling method and robust particle tracing algorithm to predict the shadow region on surfaces. To ensure the reliability and accuracy of the HACS, a rigorous verification and validation process has been systematically conducted by comparing the aerothermodynamic properties of forces, moments, and heat flux with the direct simulation Monte-Carlo (DSMC) results. The HACS is applied to the realistic geometries of VLEO satellite, the Apollo re-entry module, and spacecraft including fin and wing shapes. Results demonstrate that HACS provides the aerothermodynamic properties within the time frame of 60 seconds for the complex geometries and the accuracy of the HACS is guaranteed above 120 km altitude. The maximum relative error of the aerothermodynamic properties is less than 5% compared to the DSMC results at the lowest altitude of about 120 km, and has smaller relative errors as the altitude increases.