To investigate the penetration characteristics of ball penetrometers with various geometry characteristics in two-layered clay, large deformation finite element (LDFE) analyses incorprating modified remeshing and interpolation technique with small strain (RITSS) were conducted to simulate the ball penetration process. Soil flow mechanism and variation law of penetration resistance were analyzed. The numerical model was verified by theoretical solutions and experimental results. Through parametric analyses, the effects of top layer thickness ratio, soil strength, friction coefficient between soil and ball penetrometer, and shaft-ball area ratio on penetration characteristics were discussed. Results show that in stiff-over-soft clay, the trapped soil formed underneath the ball penetrometer was carried into the bottom layer. The size of the trapped soil was the key factor affecting the trapped soil effect. The size of the trapped soil increased with the decrease of the undrained shear strength ratio of bottom clay to top clay, and the increase of the friction coefficient between soil and ball penetrometer. The shaft-ball area ratio had certain effect on the penetration resistance, but the influence was less than those of friction coefficient and soil strength. The size was not affected by the thickness of the top layer or the undrained shear strength of the bottom clay. The thickness of the trapped soil varied from 0 to 0.20D, and the width ranged from 0 to 0.50D. The effect of trapped soil increased the penetration resistance in soft bottom clay and thus led to a larger value of the undrained shear strength. Therefore, considering the effects of soil strength, shaft-ball area ratio, and friction coefficient, a modified calculation formula was proposed to obtain more accurate results of undrained shear strength of soft bottom clay.