Precise pedestrian positioning based on smartphone-grade sensors has been a research hotspot for several years. Due to the poor performance of the mass-market Micro-Electro-Mechanical Systems (MEMS) Magnetic, Angular Rate, and Gravity (MARG) sensors, the standalone pedestrian dead reckoning (PDR) module cannot avoid long-time heading drift, which leads to the failure of the entire positioning system. In outdoor scenes, the Global Navigation Satellite System (GNSS) is one of the most popular positioning systems, and smartphone users can use it to acquire absolute coordinates. However, the smartphone’s ultra-low-cost GNSS module is limited by some components such as the antenna, and so it is susceptible to serious interference from the multipath effect, which is a main error source of smartphone-based GNSS positioning. In this paper, we propose a multi-phase GNSS/PDR fusion framework to overcome the limitations of standalone modules. The first phase is to build a pseudorange double-difference based on smartphone and reference stations, the second phase proposes a novel multipath mitigation method based on multipath partial parameters estimation (MPPE) and a Double-Difference Code-Minus-Carrier (DDCMC) filter, and the third phase is to propose the joint stride lengths and heading estimations of the two standalone modules, to reduce the long-time drift and noise. The experimental results demonstrate that the proposed multipath error estimation can effectively suppress the double-difference multipath error exceeding 4 m, and compared to other methods, our fusion method achieves a minimum error RMSE of 1.63 m in positioning accuracy, and a minimum error RMSE of 4.71 m in long-time robustness for 20 min of continuous walking.