As a significant ecological corridor from west to east across China, the Yangtze River Economical Belt (YREB) is in great need of green development and transformation. Rather than only focusing on the overall growth of green productivity, it is important to identify whether the technical change is biased towards economic performance or green performance in promoting green productivity. By employing the biased technical change theory and Malmquist index decomposition method, we analyze the green biased technical change in terms of industrial water resources in YREB at the output side and the input side respectively. We find that the green biased technical change varies during 2006–2015 at both the input side and output side in YREB. At the input side, water-saving biased technical change is generally dominant compared to water-using biased technical change during 2006–2015, presenting the substitution effects of non-water production factors. At the output side, the economy-growth biased technical change is the main force to promote green productivity, whereas the role of water-conservation biased technical change is insufficient. The green performance at the output side needs to be strengthened compared to the economic performance in YREB. A series of water-related environmental policies introduced in China since 2008 have promoted the green biased technical change both at the input side and the output side in YREB, but the policy effects at the output side is still inadequate compared to that at the input side. The technological innovation in sewage treatment and control need to catch up with the economic growth in YREB. Our research gives insights to enable a deeper understanding of the green biased technical change in YREB and will benefit more focused policy-making of green innovation.