Tungstophosphoric acid-intercalated MgAl layer double hydroxides (LDHs) are active catalysts for removing naphthenic acids (NAs) from petroleum via esterification. Due to their active sites being in the interlayer, the interlayer spacing of LDHs might affect their activity, particularly for NAs with various structures. Herein, two tungstophosphoric acid-intercalated MgAl LDHs with various interlayer spacings (d003 = 1.46 and 1.07 nm) synthesized by varying the ion-exchange time were used as catalysts for esterification between NAs and ethylene glycol. Six NAs with various side chains and rings were used as model compounds to investigate the effects of NA structures and d003 values on the activity of LDHs. In general, NAs with large molecule sizes and steric hindrances are less reactive over the same catalyst. The LDH with a larger d003 value favours the esterification of NAs regardless of their structure, particularly NAs with large molecule sizes and steric hindrances. However, a large d003 is less effective for esterification of NAs with conjugated carboxyl groups. An enlarged interlayer space might facilitate NA molecules to access the interlayer of LDHs so as to come into contact with the catalytic sites, making this process responsible for the enhanced reactivity. The esterification kinetics of cyclohexanecarboxylic acid over these LDHs follow a first-order reaction. The activation energies for the LDHs with large and small d003 values are 26.25 and 32.18 kJ mol–1, respectively.