The invention discloses a parallel alternate sampling system error estimation method based on rotation matrixes. The parallel alternate sampling system error estimation method based on the rotation matrixes comprises the following steps that (1) initial parameters are input and set; (2) training samples are built, wherein sampling sequences of M A/D conversion chips in the time quantum t are obtained, fast Fourier transform is carried out on the sampling sequences to enable the sampling sequences to be in the frequency domain, M training samples are correspondingly obtained, and a training sample set is formed by the M training samples; (3) error estimation is carried out, wherein error estimation is carried out by using a data processor and the built training sample set, and according to the process of error estimation, selection of double frequency points, covariance matrix estimation, characteristic decomposition, extraction of large characteristic values and characteristic vectors corresponding to the large characteristic values, and time-base error estimation are carried out. The parallel alternate sampling system error estimation method based on the rotation matrixes has the advantages of being small in number of the steps, reasonable in design, convenient to implement, good in using effect, and capable of effectively overcoming the defects that according to an existing parallel alternate sampling system error estimation method, the estimation process is complex, repeated iteration is needed, convergence cannot be easily carried out, the calculated amount is large, and the local minimum point can be easily generated.