We estimate variations of the crustal thickness beneath the Nepal Himalayas based on tomographic inversion of regional earthquake data. We have obtained a low-velocity anomaly in the upper part of the model down to depths of 40 to 80 km and proposed that the lower limit of this anomaly represents variations of the Moho depth. This statement was supported by results of synthetic modeling. The obtained variations of crustal thickness match fairly well with the free-air gravity anomalies: thinner crust patterns correspond to lower gravity values and vice versa. There is also some correlation with magnetic field: higher magnetic values correspond to the major areas of thicker crust. We propose that elevated magnetic values can be associated with more rigid segments of the incoming Indian crust which cause more compression in the thrust zone and lead to stronger crustal thickening.