This work provides quantified explanations for the thermodynamic and kinetic characteristics of esterification in aqueous phase, and how phase transfer catalysts improve water phase esterification of fatty acids in a computational-experimental way. Self-catalyzed reaction mode with or without solvation effects, water participated reaction mode, and catalytic reaction mode (catalyzed by p-dodecyl benzene sulfonic acid, DBSA) are discussed. Our results show that the initial self-catalytic reaction mode undergoes the energy barrier of 100.1 kJ/mol, and rises to 148.9 kJ/mol when water molecule is involved, which hinders the esterification reaction. With the DBSA catalyst, this energy barrier will drop to 97.5 kJ/mol and the water phase esterification is successfully promoted with the yield of 81%. The key kinetic factor of binding energy is discussed as that water molecule has a strong reactant binding competitiveness (with the binding energy of -57.9 kJ/mol, and the value for the non-aqueous phase mode is 3.0 kJ/mol) and DBSA has the binding energy with the value of -45.3 kJ/mol, so it can compete with water to form reactant complexes. This work is a successful practice of a computation-experiment combined scheme, and provides a quantitative basis for the improvement of phase transfer catalysts on water phase esterification reactions. The calculation mode and method of aqueous esterification make it possible to convert bio-based fatty acids into fatty acid esters in fermentation broth.