The invention provides an OFDM-IM system frequency offset estimation method. The method comprises the steps of S1, using a two-step method to perform preliminary frequency offset compensation on a receiving signal that is subjected to non-uniform frequency offset: 1, resampling and down-converting; and 2, performing unified compensation on the residual frequency offset (epsilon), wherein the sum of energy for using null sub-carriers used in the sub-step 2 is used as a cost function, a preliminary estimated value of the epsilon is acquired via one-dimensional search, and preliminary compensation is performed; S2, estimating a non-activated sub-carrier position in an OFDM-IM system by using the preliminarily compensated signal; and S3, endowing each estimated sub-carrier with a certain weight, adding the energy of the estimated sub-carriers into the cost function according to the different weights, performing the one-dimensional search on the epsilon to acquire a final estimated value ofthe epsilon, and performing compensation once more. According to the method provided by the invention, the sub-carriers using the OFDM-IM are partially activated. It means that the energy of the non-activated sub-carriers can still be used besides the preliminarily set null sub-carriers. Therefore, the estimation of Doppler frequency shift is optimized by using the non-activated sub-carriers.