A novel compensation scheme for timing synchronization error in GPP-SDR LTE system is proposed in this article. The properties of timing synchronization error are analyzed, and it is exploited to design a compensation scheme suitable to GPP-SDR baseband processing capacity. Furthermore, the applicability of the scheme is assessed in theory analysis and tested by simulations and experiments. It is revealed from the results that the BER of baseband processing with timing synchronization error compensation is about 10−4 while that without compensation is about 0.1.