Accurate pedestrian navigation remains a challenge in urban environments. GNSS receiver behaves poorly because the reflection and blockage of the GNSS signals by buildings or other obstacles. Integration of GNSS positioning and Pedestrian Dead Reckoning (PDR) could provide a more smooth navigation trajectory. However, the integration system cannot present the satisfied performance if GNSS positioning has large error. This situation often happens in the urban scenario. This paper focuses on improving the accuracy of the pedestrian navigation in urban environment using a proposed altitude map aided GNSS positioning method. Firstly, we use consistency check algorithm, which is similar to receiver autonomous integrity monitoring (RAIM) fault detection, to distinguish healthy and multipath contaminated measurements. Afterwards, the erroneous signals are corrected with the help of an altitude map. We called the proposed method altitude map aided GNSS. After correcting the erroneous satellite signals, the positioning mean error could be reduced from 17 meters to 12 meters. Usually, good performance for integration system needs accurately calculated GNSS accuracy value. However, the conventional GNSS accuracy calculation is not reliable in urban canyon. In this paper, the altitude map is also utilized to calculate the GNSS localization accuracy in order to indicate the reliability of the estimated position solution. The altitude map aided GNSS and accuracy are used in the integration with PDR system in order to provide more accurate and continuous positioning results. With the help of the proposed GNSS accuracy, the integration system could achieve 6.5 meters horizontal positioning accuracy in urban environment.