Halotolerant endophytic fungi (HEFs) represent a critical biological resource in mitigating plant salt–alkali stress, demonstrating remarkable adaptability across diverse ecological environments. This comprehensive review analyzes 150 scientific publications, revealing HEFs’ multifaceted mechanisms of plant stress tolerance. Inhabiting over 30 host plant species without causing pathogenic effects, these fungi enhance plant resilience through sophisticated physiological strategies. Key findings highlight HEFs’ ability to modulate ionic homeostasis, elevate antioxidant capacities, and stimulate plant growth under saline conditions. The research unveils the potential of HEF metabolites as biostimulants and explores their co-evolutionary hypotheses with host plants. Despite promising laboratory and field validations, significant challenges remain in HEFs’ practical agricultural applications, including environmental factor interactions and biotechnological ethical considerations. Future research directions emphasize deeper investigations into HEFs’ ecological adaptability and microbiological interactions to unlock their full agricultural potential.