In the field of map matching, algorithms using topological relationships of road networks along with other data are normally suitable for high frequency trajectory data. However, for low frequency trajectory data, the above methods may cause problems of low matching accuracy. In addition, most past studies only use information from the road network and trajectory, without considering the traveler’s path choice preferences. In order to address the above-mentioned issue, we propose a new map matching method that combines the widely used Hidden Markov Model (HMM) with the path choice preference of decision makers. When calculating transition probability in the HMM, in addition to shortest paths and road network topology relationships, the choice preferences of travelers are also taken into account. The proposed algorithm is tested using sparse and noisy trajectory data with four different sampling intervals, while compared the results with the two underlying algorithms. The results show that our algorithm can improve the matching accuracy, especially for higher frequency locating trajectory. Importantly, the method takes into account the route choice preferences while correcting deviating trajectory points to the corresponding road segments, making the assumptions more reasonable. The case-study is in the city of Beijing, China.