In order to better understand transition zones with a variety of structural features that affect thin varying thickness strips, 6061 aluminium alloy thin strips were flexibly rolled into different thickness ratios and transition zone lengths, using an innovative micro rolling mill. The microstructure and mechanical properties of the thin varying thickness strips produced by micro flexible rolling were systematically investigated and the mechanisms were analysed. The results indicate that a thin varying thickness strip with either a larger thickness ratio or a shorter transition zone length will present a relatively high slope of the transition zone during micro flexible rolling. After tensile tests, a thin varying thickness strip with the highest thickness ratio achieved the largest yield strength and ultimate tensile strength. In comparison, transition zone length can have a greater influence on the strain of the transition zone than on the thickness ratio because of the variation in β. The measured hardness is greater in the thinner zone than in the thicker zone. Values in the thinner zone are about 7%–21% greater than those in the thicker zone for strips with different thickness ratios due to the increased strain level which causes different degrees of work hardening.