The effect of beat noise in a time domain optical coherence tomography (OCT) system was investigated through theoretical analysis and their comparision with experimental data. It is shown that the best SNR of a fiberbased and balanced OCT system is about 100 dB, being restricted by the beat noise. And, the excess intensity noise may not be eliminated completely in a practical balanced OCT system, and this leads to a SNR value of 10~20 dB lower than the theoretically expected value. A simplified physical model that describes the overall noise of a time domain OCT system was established. By using such a model, the influence of the optical interferemeter, signal filtering and amplifier circuits, the resolution of data acquisition system and the external electromegnetic interference source were analyzed on the overall signaltonoise raitio of a practical optical coherence tomographic system, presenting a useful method to optimize the performance of the interested OCT system.