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Seepage analysis is the central issue in solving the unconfined seepage problems from complex earth‐rock dams. The precision and efficiency of seepage simulation are the major technical barriers to exploring the heterogeneities of hydrological state variables in dams. This paper addresses the heterogeneity of the saturated‐unsaturated zones of dams and develops the smoothed finite element method (S‐FEM) capable of solving the seepage problem in domains with arbitrary geometry and continuously varied permeability. The gradient smoothing technique, in which the area integrals are transformed into the line integrals around edges of smoothing cells, is used to obtain the element matrices, which is used to simplify the solution of seepage problem. To be specific, we employ Van Genuchten method to modify the hydraulic conductivity of unsaturated zones medium and Signorini condition to convert the outflow boundary into the water head boundaries. The precision of the proposed method together with the importance of considering the unsaturated zones are first deliberated by the verification tests. Then, to quantify the impacts on the hydrological state variables, we focus on the heterogeneity of the entire zones through exploratory tests. The results show that the presence of leakage anomalies and auxiliary dam structures has a significant effect on the redistribution of hydrological state variables, which convinces that the findings may lay the foundation for the development of multi‐parameter seepage inversion and the derivation of coupled hydro‐geophysical inversion using the most appropriate starting model. [ABSTRACT FROM AUTHOR]