Precise trajectory control is imperative to ensure the safety and efficacy of in vivo therapy employing the magnetic helical millirobots. However, achieving accurate 3-D path following of helical millirobots under fluid flow conditions remains challenging due to the presence of the lumped disturbances, encompassing complex fluid dynamics and input frequency saturation. This study proposes a robust 3-D path following control framework that combines a disturbance observer for perturbation estimation with an adaptive finite-time sliding mode controller for autonomous navigation along the reference trajectories. First, a magnetic helical millirobot's kinematic model based on the 3-D hand position approach is established. Subsequently, a robust smooth differentiator is implemented as an observer to estimate disturbances within a finite time. We then investigate an adaptive finite-time sliding mode controller incorporating an auxiliary system to mitigate the estimated disturbance and achieve precise 3-D path tracking while respecting the input constraints. The adaptive mechanism of this controller ensures fast convergence of the system while alleviating the chattering effects. Finally, we provide a rigorous theoretical analysis of the finite-time stability of the closed-loop system based on the Lyapunov functions. Utilizing a robotically-actuated magnetic manipulation system, experimental results demonstrate the efficacy of the proposed approach in terms of the control accuracy and convergence time.