We applied ab initio phonon analysis to layered titanium-oxypnictides, Na(2)Ti(2)Pn(2)O (Pn = As and Sb), and found a clear contrast between the cases with lighter/heavier pnictogen in comparison with experiments. The result completely explains the experimental structure at low temperature, C2/m for Pn = As, within the conventional charge density wave, while there arise discrepancies when the pnictogen gets heavier. Our phonon calculation using the GGA-PBE functional predicts that a Cmce polymorph is more stable than the experimentally observed one (Cmcrn) for Pn = Sb. On the basis of further quantitative analysis, we suggest the possibility that the GGA-PBE functional does not properly reproduce the electron correlation effects for Pn = Sb, and this could be the reason for the present discrepancy.