Commuting contributes to high levels of greenhouse gases and air pollution. The recently advocated ‘green commuting’, i.e. active and public modes of transport, will be conducive to low-carbon and environmentally friendly transport. A baseline goal of urban planning is to promote health; however, few studies have explored the health-related impacts of environments at both ends of the commute on residents’ commuting mode choices. To fill the gap, this study proposes to consider the impact of the neighbourhood and working environment on green commuting from a health perspective. Using a sample of 15,886 people from 368 communities in China, three generalised multilevel linear regression models were estimated. Physical and psychological health were combined to further analyse health-related environmental attributes on the commuting choices of residents with different health levels. The results indicate that the working environment exerts more substantial effects on ‘green commuting’ than the neighbourhood environment, especially for workplace satisfaction. Moreover, we found that a good working environment and relationships will significantly encourage the sub-healthy group to choose active commuting. These findings are beneficial for policymakers to consider focusing on reconciling neighbourhood and working environments and meeting the commuting requirements of the less healthy group.