The failure to achieve minimum design overlap between secant piles compromises the ability of a structure to perform as designed, resulting in water leakage or even ground collapse. To establish a more realistic simulation and provide guidelines for designing a safe and cost-effective secant-pile wall, a three-dimensional model of a secant pile, considering the geometric imperfections of the diameter and direction of the borehole, is introduced. An ultrasonic cross-hole test was performed during the construction of secant piles in a launching shaft in Beijing, China. Based on the test results, the statistical characteristics of the pile diameters and orientation parameters were obtained. By taking the pile diameter D, inclination angle β, and azimuth angle α as random variables, Monte Carlo simulations were performed to discuss the influence of different design parameters on the probability density functions of the overlap of secant piles. The obtained results show that the randomness of the inclination angle and pile diameter can be well described by a normal distribution, whereas the azimuth angle is more consistent with a uniform distribution. The integrity of the secant-pile wall can be overestimated without considering the uncertainty of geometric imperfections. The failure of the secant-pile wall increases substantially with increasing spatial variability in drilling inclination and diameter. A design flowchart for pile spacing under the target safety level is proposed to help engineers design a safe and economical pile wall.