In previous studies, traditional GNSS (global navigation satellite system) ionospheric tomographic methods neglect the influence of geomagnetic field on the ionospheric variations. In this method, a new GNSS tomographic algorithm with the unequal pixel size in the height was proposed to image the ionosphere in the geomagnetic coordinate, which takes into account the influence of electron density variation at different ionospheric heights and the geomagnetic field. Also, a new iterative relaxation factor was established in the proposed GNSS tomographic algorithm to improve the accuracy of the ionospheric electron densities. The performance of GNSS ionospheric tomographic method with unequal pixel size considering geomagnetic effects was evaluated by using the IRI—2007 (international reference ionosphere 2007) model, GNSS measured data, and ionosonde data. For simulation studies, IRI—2007 was used as references, while for GNSS data, the ionosonde data were used as references. The peak ionospheric electron density error, the average absolute percentage error of electron density profile results and the root mean square error were estimated by different GNSS tomographic algorithms. The validity of the tomographic algorithm with the unequal pixel sizes considering the geomagnetic effects is verified.