This study adopts a spatial perspective to analyse the complex commuting patterns of the Beijing metropolitan region. By combining measures of the built environment, neighbourhood characteristics and development time periods, a four-fold neighbourhood classification was derived by cluster analysis to reflect different urbanisation contexts. Commuting flows analysis was mapped to illustrate the spatial mismatch of home-work locations during the rampant urbanisation process. The novel use of multi-level modelling approach shows how individual socio-economic attributes and neighbourhood factors, and their interactive effects, explain the varied commuting patterns. The cross-level interactions of variables highlight the predominant influence of individual attributes, which also interact with locational conditions of neighbourhood with differential explanatory power, on commuting patterns.