The Flight Management System (FMS) on civil aircraft takes responsibility for flight planning, position calculation, performance calculation, and flight guidance. Performance Database (PDB) stores necessary aircraft-specific performance data to allow FMS to carry out the related functions. To solve the PDB compliance issue, the first-principal design method in the PDB development process is introduced to allow more accurate trajectory prediction in complex flight scenarios. In this method, PDB includes full engine performance data, performance limits, and aerodynamic data. To ensure the database quality and integrity, the methods of combining the element-level testing and system-level functional verification are investigated to demonstrate the onboard PDB satisfies the system function, performance, and airworthiness requirements based on engineer practice.