Accurate and smooth global navigation satellite system (GNSS) positioning for pedestrians in urban canyons is still a challenge due to the multipath effects and the non-light-of-sight (NLOS) receptions caused by the reflections from surrounding buildings. The recently developed factor graph optimization (FGO) based GNSS positioning method opened a new window for improving urban GNSS positioning by effectively exploiting the measurement redundancy from the historical information to resist the outlier measurements. Unfortunately, the FGO-based GNSS standalone positioning is still challenged in highly urbanized areas. As an extension of the previous FGO-based GNSS positioning method, this paper exploits the potential of the pedestrian dead reckoning (PDR) model in FGO to improve the GNSS standalone positioning performance in urban canyons. Specifically, the relative motion of the pedestrian is estimated based on the raw acceleration measurements from the onboard smartphone inertial measurement unit (IMU) via the PDR algorithm. Then the raw GNSS pseudorange, Doppler measurements, and relative motion from PDR are integrated using the FGO. Given the context of pedestrian navigation with a small acceleration most of the time, a novel soft motion model is proposed to smooth the states involved in the factor graph model. The effectiveness of the proposed method is verified step-by-step through two datasets collected in dense urban canyons of Hong Kong using smartphone-level GNSS receivers. The comparison between the conventional extended Kalman filter, several existing methods, and FGO-based integration is presented. The results reveal that the existing FGO-based GNSS standalone positioning is highly complementary to the PDR's relative motion estimation. Both improved positioning accuracy and trajectory smoothness are obtained with the help of the proposed method.