In 3GPP LTE (long term evolution) physical layer protocol, Both CQI (channel quality indicator) and HARQ-ACK (hybrid automatic repeat request acknowledgement) adopted a method called super code based on Reed-Muller. It is similar to the encoding of TFCI (transport format combination indicator) in TD-SCDMA physical layer protocol. But the coding matrix used more complex interleaver technology and increased more masks in 3GPP LTE. It made receiver s decoding difficult. According to the characteristics of coding matrix, this paper used FHT (fast Hadamard transformation) and gave an effective decoding algorithm of Reed-Muller. Simulation results show the effectiveness of the algorithm, which has been applied to LTE-TDD wireless integrated test instrument.