Auto-search is one of the key steps in digital signal processing for Loran-C receivers, however, for digital sampling Loran-C signal, the principle search algorithm is unable to realize signal search veraciously because of the asynchronism between sampling clock and transmitting station clock. For this question, an auto-search algorithm based on subsection correlation for Loran-C is presented after analyzing the principle search algorithm. The experiment results show that for the received digital Loran-C signal, there are several correlation and accumulation values of master and secondary stations to exceed the search thresholds; the maximum correlation and accumulation value of the presented algorithm is far higher than that of the principle algorithm. That is to say, the presented algorithm can search the arrival time of master and secondary station successfully, solve the problem of clock asynchronism effectively, and enhance the search sensitivity of the receiver, which have great significance for digital processing of Loran-C signal and the engineering realization of Loran-C digital receiver.