•The Leeuwin Current became stronger after the Mid-Pleistocene Transition.•Stronger Leeuwin Current was mainly triggered by enhanced atmospheric circulation.•Stronger Leeuwin Current has not overturned the Pliocene-Pleistocene drying trend. Although the Leeuwin Current (LC) is thought to play a pivotal role in climatic and oceanic systems of the western Australian region, how the LC developed through the Pliocene-Pleistocene period remains elusive. Here we used biomarker records to reconstruct variations of temperatures and primary productivity on the northwest shelf of Australia over the last 6 million years. Since ∼1.2 million years ago (Ma), our sea surface temperature record indicates progressive warming, with temperature values comparable to those in the Indo-Pacific Warm Pool, in contrast with the long-term global cooling trend. The regional surface warming was accompanied by suppressed primary productivity, together indicating prevailing warm, low-salinity, nutrient-deficient surface water, and thus a stronger LC since the Mid-Pleistocene Transition. During 4–1.2 Ma, greater surface temperature gradient between the Indo-Pacific Warm Pool and the northwest shelf of Australia and higher primary productivity seem to suggest a generally weaker LC. Warmer temperatures and lower productivity suggest a plausible existence of the LC during 6–4 Ma, but more work is required to confirm this. Impact of sea level and the Indonesian Throughflow on the LC strength may exist, but did not dominate through the Pliocene-Pleistocene period, considering different variation patterns among them. We propose the stronger LC after ∼1.2 Ma was more likely triggered by enhanced atmospheric circulation. Although the increased LC after ∼1.2 Ma may have potentially brought additional moisture to the Australian continent during the interglacial periods, it has not overturned the long-term drying trend through the Pliocene-Pleistocene period.