In chip-based quantum key distribution (QKD) systems, the non-ideal quantum state preparation due to the imperfect electro-optic phase modulators (EOPM) decreases the secret key rate and introduces potential vulnerabilities. We propose and implement an on-chip transmittance-invariant phase modulator (TIPM) to solve this problem. Simulated and experimental results show that TIPM can eliminate the correlation between phase, intensity, and polarization of quantum states caused by phase-dependent loss. The design can tolerate a significant fabrication mismatch and is universal to multi-material platforms. Furthermore, TIPM increases the modulation depth achievable by EOPMs in standard process design kit (PDK). The proposal of TIPM can improve the practical security and performance of the chip-based QKD systems.