A method for estimating the indoor height of pedestrians based on micro pressure sensors was developed to address the issues of errors accumulated over time in the height calculations performed using the current pressure sensors. In this method, based on the output height value of a micro pressure sensor, an algorithm judges the height values of multiple adjacent time points. It constrains the height change based on the indoor pedestrian movement status such that this change conforms to the indoor pedestrian movement law. Simulations were performed using data from a MS6511 micro pressure sensor. Experimental results indicate that the proposed method effectively corrected height errors. As compared with the height errors calculated using micro pressure sensor data, the trajectories calculated with the proposed method were closer to the real ones. The average closed-loop error decreased from 1.9%D to 0.07%D, effectively improving the positioning accuracy of indoor pedestrian height estimation. This method has engineering application value in the field of indoor 3D pedestrian positioning.