Molecular vibration of several modes in blue-phase polydiacetylene-3-butoxycarbonylmethylurethane (PDA-3BCMU) was real-time observed by 5-fs pump-probe measurement. The contribution of the vibrational wavepackets in the ground state and in the excited state in the signal were separated by multichannel measurements The C equivalent to C stretching mode in the ground state starts to oscillate p-out-of-phase with the C equivalent to C stretching mode. The structure of PDA-3BCMU in the geometrically relaxed state is not pure butatriene-type but more like acetylene-type. The frequencies of C equivalent to C and C equivalent to C stretching modes there were determined by singular value decomposition method to be 1472 +/- 6 cm(-1) and 2092 +/- 6 cm(-1) , respectively. The double and triple bond stretching frequencies in the ground state which are 1463 +/- 6 cm(-1) and 2083 +/- 6 cm(-1) , respectively.