We use magnetic field data observed by the Swarm mission from 2014 to 2020 to construct, for the first time, a two-dimensional (2D) lithospheric magnetic anomaly model of Egypt and its surrounding area. Nighttime data during quiet geomagnetic conditions has been expanded in terms of the Legendre polynomial in harmonic terms N = 6–50. The damped least square method has been used to estimate the model coefficients based on the lithospheric magnetic data. Modeled data at two different altitudes (438–448 km and 503–511 km) were compared with the CHAOS model. Results exhibit that the 2D model is superior to the CHAOS model in the capability of extracting more information about small-scale crustal anomaly field. At low altitudes (438–448 km), the strength of the anomaly field increases, but the noise of the external fields has greatly reduced at high altitudes (503–511 km). Besides, the magnetic anomaly field at low altitudes has illuminated short-scale anomalies that didn't appear at high altitudes. Both the total and vertical magnetic anomaly vectors showed their ability to reveal tectonic structures compared with Moho depth map and the geological maps.