Improving the tolerance of channel noise is an important task for devising and implementing quantum key distribution (QKD) protocols. Quantum phase-flip error rejection (QPFER) code [Phys. Rev. Lett.92, 077902 (2004)PRLTAO0031-900710.1103/PhysRevLett.92.077902] has been introduced by Wang to increase the tolerable phase-flip noise of QKD implementations. However, an experiment that demonstrates its advantages is still missing. Here, we experimentally verify the QPFER code with the assistance of two photon quantum states generated by spontaneous parametric downconversion. The methods of parity check and postselection are introduced to the protocol for achieving the phase-flipping rejection. Comparing with the standard realization of the single photon polarization encoding BB84 scheme, the quantum error rate after decoding is obviously reduced when the probability of channel noise is less than 25%. The experiment results also show that QPFER protocol can reduce error rate, obtain a higher key rate, and be robust in the noisy channel when the noise level is in a proper region.