Variable-geometry turbines present significant improvements in both off-design cycle efficiency and enhanced engine responsiveness for future adaptive cycle engines. The adjustable vanes regulate the through-flow capacity by varying the installation angle and thus unavoidably require endwall clearance, resulting in profound implications for vane and downstream blade rows. Unsteady numerical simulations are carried out to investigate the vane-rotor flow interaction under the zero and partial clearance type of the adjustable vane in a 1.5-stage variable-geometry turbine. First, specific vortical structures and loss characteristics of upstream adjustable vane leakage flow at turning angles of −5°, 0°, and +5° are described. Then, the basic mechanisms of vane-rotor secondary flow interaction between acquired upstream leakage flow and downstream blade rows secondary flow is explored by the time-resolved method and quantitative detailed analysis method. The results show that adjustable vane vortex core area is the primary cause of internal loss within the vortex, and the mixing and interaction between the leakage vortex and other vortex systems contribute to secondary loss in the vane. Due to the downstream blade shear action caused by different flow velocity on the suction and pressure surfaces, the vane leakage flow fragments upon entering the R1 blade passage and develops downstream of the endwall region. Compared to the vane with zero clearance case at same turning angle, the intensity of the R1 tip leakage vortex at the design turning angle and open turning angle is reduced by 47.4 % and 23.66 % with the upstream partial clearance, respectively. The unsteady vane-rotor secondary flow interaction under different turning angles has large influence on the flow structure and loss characteristics of the downstream blade rows, and results in significant differences in the variation pattern and trend direction of the turbine performance.