Considering the situation that the received signals magnitude is decreased and inter-carrier interference (ICI) is induced by the carrier frequency offsets (CFO), through establishing mathematical model, the analytical expression for the Bit Error Rate (BER), which is derived from Transform Domain communication system (TDCS), is obtained. Furthermore, the relationships between the BER and the correlated parameters are studied, as well as, the Signal Noise Ratio (SNR) loss. Finally, the analysis conclusions are verified by the simulation, the simulation result agrees well with the analysis conclusion. The quantitative analysis of the system performance caused by the frequency error of carrier is given. These researches illustrate that the frequency offset affect the BER performance seriously and there is error floor on the BER when the normalized frequency offset is more than 0.6.To keep the system work around, the normalized frequency offset has to be less than 0.05.