Abstract: By utilizing fully the shared L3 Cache, private L2 Cache and L1 Cache on the multi-core architecture, the produced large-scale data with the different combination of positions are distributed to the multi-level caches while the Modeling algorithm is used to solve (l,d)-Motif finding problem, and a cache-efficient thread-level parallel (l,d)-Motif finding algorithm is designed on multi-core computer by binding the threads to the cores to balance their computational loads. The experimental results show that, compared with the existing parallel algorithm to solve (l,d)-Motif finding problem, the presented algorithm is efficient and has good speedup and scalability, and it can solve successfully the (l,d)-Motif finding problem with longer l.