Thin strips with varying thicknesses (TSVTs) produced by micro flexible rolling have wide applications in diverse micro manufacturing areas such as micro electromechanical systems (MEMS) and micro system technologies (MST). TSVTs consist of three regions based on different thicknesses, i.e. the thicker, the transition and the thinner zones. Among them, the transition zone plays a key role in evaluating the quality of TSVTs. In the current work, thin 1060 aluminium alloy strips were flexibly rolled under various thickness ratios followed by annealing treatment. The influences of annealing temperature on the microstructural evolution and hardness variation of the transition zone of TSVTs were investigated. The results reveal that the recrystallisation has happened after annealing at 400 °C for 30 min, which induces fine and homogeneously-distributed grains in both of the thinner and transition zones. Only moderate increase in hardness is found from the thicker to the thinner zones after annealing treatment.