The urgent need to develop low carbon urban transport systems particularly in Asian megacities is facing the significant challenge of growing motorization following population increase and economic development. Sustainable urban public transport (UPT) plays a crucial role to fulfil the ambitious targets on carbon emission reduction. In this study, life cycle assessment was employed to quantify the environmental impacts (measured by carbon emissions) of UPT systems (including bus and subway) in Shenzhen, a leading megacity in South China, and then to examine corresponding carbon intensity reduction potentials. Results showed that the total carbon emissions from UPT in Shenzhen have increased rapidly from 0.70 Mt in 2005 to 1.74 Mt in 2015 due to the fast growth of the volume of transport turnover. However, current low-carbon UPT mode has only reduced 0.21 Mt CO2 e (cumulative value, from 2005 to 2015), and thus could not contribute proportionally to the city's overall emission reduction target. Three advanced scenarios (from conservative to optimistic) were further simulated to estimate carbon emissions and their intensity reduction potentials over the next 15 years (2016–2030). Compared to the business-as-usual scenario, all these three low-carbon transition scenarios could significantly mitigate the rapid growth of carbon emissions and consequently help achieve Shenzhen's carbon intensity reduction goal by 2030 (60%, compared to 2005 level). These findings could not only inform evidence-based policy making to facilitate the low-carbon transition of the urban transport sector in Shenzhen, but also shed light on sustainable urban transition in other megacities.