Aiming at the timing synchronization difficulty of LDPC-coded system on GF(q) in deep space communication, a new soft timing synchronization algorithm is proposed. Firstly one cost function using the soft decoding information of LDPC on GF(q) is introduced for coarse timing synchronization, then the Expectation-Maximum algorithm is used for fine timing synchronization based on the maximum likelihood criterion. Conducting the joint iteration of timing synchronizer, demodulator and decoder, the soft information provided by LDPC decoder is used to aid the timing estimation, and the timing estimation close to the modified Cramer-Rao bound can be obtained by interpolation of the over-sampled data. Simulation results show that, at low SNRs, the efficient timing synchronization can be achieved with large timing offset, and almost ideal performance is obtained with low system complexity.