The rapid advancement of quantum computing poses a substantial threat to classical cryptographic systems, accelerating the global shift toward post-quantum cryptography (PQC). Despite their theoretical robustness, practical deployment of PQC algorithms remains hindered by challenges such as computational overhead, side-channel vulnerabilities, and poor adaptability to dynamic environments. This study integrates machine learning (ML) techniques to enhance three representative PQC algorithms: FrodoKEM, Falcon, and Supersingular Isogeny Key Encapsulation (SIKE). ML is employed for four key purposes: performance optimization through Bayesian and evolutionary parameter tuning; real-time side-channel leakage detection using deep learning models; dynamic algorithm switching based on runtime conditions using reinforcement learning; and cryptographic forensics through anomaly detection on vulnerable implementations. Experimental results demonstrate a reduction of up to 23.6% in key generation time, over 96% accuracy in side-channel detection, and significant gains in adaptability and leakage resilience. ML models also identified predictive patterns of cryptographic fragility in the now-broken SIKE protocol. These findings confirm that machine learning enhances both performance and security, enabling intelligent and adaptive cryptographic infrastructures for the post-quantum era.