As a new class of porous crystalline materials, hydrogen-bonded organic frameworks (HOFs) assembled from building blocks by hydrogen bonds have gained increasing attention. HOFs benefit from advantages including mild synthesis, easy purification, and good recyclability. However, some HOFs transform into unstable frameworks after desolvation, which hinders their further applications. Nowadays, the main challenges of developing HOFs lie in stability improvement, porosity establishment, and functionalization. Recently, more and more stable and permanently porous HOFs have been reported. Of all these design strategies, stronger charge-assisted hydrogen bonds and coordination bonds have been proven to be effective for developing stable, porous, and functional solids called hybrid HOFs, including ionic and metallized HOFs. This Review discusses the rational design synthesis principles of hybrid HOFs and their cutting-edge applications in selective inclusion, proton conduction, gas separation, catalysis and so forth.