Study of constraints of stock emplacement and geometry on associated skarn orebodies is significant for the understanding of the epithermal deposit system. We have chosen the typical Tongguanshan skarn ore deposit (eastern China) as our target area. The Tongguanshan stock was emplaced at the NE–SW-striking Tongguanshan anticline and is characterized by macroscopically homogeneous quartz–monzodiorite. The magnetic parameters show that the stock is dominated by oblate magnetic ellipsoids and a high degree of anisotropy (> 1.1), and this value is higher at the stock margin. The strike of magnetic foliation at the stock margin is parallel to the stock boundary with sub-horizontal magnetic lineations. A vertical NE–SW-striking magnetic foliation, which is parallel to the regional structures, is revealed inside the stock. The three-dimensional geometric modelling shows that the stock has a tongue-like geometry and the contact surface in both eastern and western sides dips to the NW, but the western side is steeper. Nevertheless, the orebodies are almost developed at the eastern side. Accordingly, we propose that the Tongguanshan stock was constructed by multiple magma pulses, initiated at the SW part of the stock, and ascended along inherited NE–SW extended fractures in the Tongguanshan anticline. The successive magma pulses either accreted by a unilateral E-wards trend or by bilateral magma accretion, which resulted in a deformation difference in the contact zone and caused uneven orebody development. Our study also shows that the strike, dip angle and curvature situation of contact surface, which affects the water–rock reaction process and distribution of the dilation zone, are important ore-controlling factors.