Based on the intelligent substation development, this paper analyzes the influence of unsynchronized sampling value (SV) on differential protection under the circumstance of substation information sharing, based on which a substation differential protection algorithm based on phase set is proposed. The algorithm uses the current synchronous phasor reference citation of each branch for differential protection logic calculation, and the calculated differential current and braking current can solve protection malfunction or refuse caused by the unsynchronized SV. Finally, the simulation results show that using the differential protection algorithm based on phase set, the sensitivity and reliability are not affected under a certain extent unsynchronized SV, which ensures reliable implementation of substation differential protection. Therefore, this differential protection algorithm can be used in the new generation intelligent substation.