The requirements of the clock synchronous system in the smart substation is much higher compared with traditional substations. The influence of synchronization quality depending on output data of the merging unit（MU） different type protections is analyzed. It should be pointed out that the synchronization quality of the data has great influence on main protection， but has less effect on backup protection which only depends on signal magnitude. As the clock source receiving satellite signals is influenced by the weather and other factors， it may cause the spike of output clock signal， so that out of step at same time may happen to all equipments of substation. In such case MU should output continuously stable data with synchronization quality， in order to reduce the effect on protection equipment. Measures must be taken to ensure the quality of the output data. A detailed analysis about MU countermeasures on abnormal situation of synchronous pulse is described in the paper. It is pointed out that inconsistencies of the synchronous tracking method of the different MU may seriously affect the safe operation of the protections. The unified standard of the synchronous problem processing must be strictly implemented by MU manufacturers.