The present study focuses on probing the extent to which nonlinear optical effects act as a guide to protonation sites of alpha-Keggin heteropolyanions [SiW12O40](4-) and [SiV3W9O40](7-) The second-harmonic generation (SHG) values of differently protonated forms predict that the molecular nonlinear optical activity has a close relationship with protonation sites and provides a new potential experimental probe.