Section linking aims at relating structural units in the notation of a piece of music to their occurrences in a performance of the piece. In this paper, we address this task by presenting a score-informed hierarchical Hidden Markov Model (HHMM) for modeling musical audio signals on the temporal level of sections present in a composition, where the main idea is to explicitly model the long range and hierarchical structure of music signals. So far, approaches based on HHMM or similar methods were mainly developed for a note-to-note alignment, i.e. an alignment based on shorter temporal units than sections. Such approaches, however, are conceptually problematic when the performances differ substantially from the reference score due to interpretation and improvisation, a very common phenomenon, for instance, in Turkish makam music. In addition to having low computational complexity compared to note-to-note alignment and achieving a transparent and elegant model, the experimental results show that our method outperforms a previously presented approach on a Turkish makam music corpus.