Aquitard with uneven thickness and discontinuities commonly occurs in thick-overburden dam base in Northwest China. The seepage field in dam foundation is affected by the thickness, discontinuity form and opening size of the aquitard, which is needed to be studied in depth. In this paper, based on the seepage theory of unsaturated soil and seepage solution in Seep/w, we aim to obtain the influence of thickness and continuity of a aquitard in the middle position on the discharge per unit width and exit gradient, and compare with engineering practices. Results show that discharge per unit width and exit gradient decrease as the aquitard thickness increases. The influence of aquitard thickness on seepage field decreases in order of semi-closed cut-off wall, suspended cut-off wall and totally enclosed cut-off wall. The semi-closed joint anti-seepage system formed by aquitard and cut-off wall at the upstream is of the best control effect, followed by aquitard that opens at the downstream, case in which opens at both the upstream and downstream is the worst. The discharge per unit width and exit gradient increase with the opening length of aquitard. But at the upstream seepage system, since the weak layer only plays a weak role in water separation, therefore the opening length has little influence on seepage field. It is suggested that a semi closed joint anti-seepage system formed by cut-off wall and downstream aquitard is a doable measure, which can avoid the adverse condition that opens of aquitard both at the upstream and downstream. It is found that, compared with the monitoring result, the simulating error meets the codes. Therefore, the calculation method and conclusions of this paper are reliable.