Public facilities capitalization of formal housing has been widely discussed. However, how residents of informal housing value facilities and how they differ from formal housing remain unclear. We employ hedonic model and the gradient boosting decision trees approach to address the gap by identifying the differences between small property rights housing (SPRH) and commercial housing in Shenzhen, China. Empirical modeling results reveal that the capitalization effects of public facilities in SPRH are significantly lower than in commercial housing. SPRH buyers are significantly less willing than those commercial housing buyers to pay for public facilities, and the gap in willingness to pay between these two types of housing buyers is greater for public middle schools with access related to housing tenure than for metro stations and hospitals. After accounting for how the poor public facility provision of SPRH affects capitalization effects, we further find that informal tenure weakens SPRH capitalization effects. These findings help planners and policymakers better understand the housing market so they can take reasonable initiatives to make urban public facilities more accessible and urban housing systems more affordable, further improving the sustainability of urban areas.