The classification of noise in the returned signal of residual turbulent scintillation(RTS) lidar was introduced. Based on changing condition of experimental status, the amplitude and variance of different sum of the baseline of A/D card, amplifier, PMT, background noise and shot noise were acquired. By comparison of different noise, it is found that the baseline of amplifier is primary and background noise is small when telescope doesn’t receive atmospheric scattering signal. When telescope receives scattering signal, the shot noise is primary in near range (2 km for near channel and 4 km for far channel), and is small in far range. The experiment results show different impact of different noise on total noise, and so are instructive on acquiring atmospheric turbulence form returned signal of RTS lidar, as well as reducing influence of noise on effective signal.