The intensity of human activity, habitat loss and habitat degradation have significant impacts on biodiversity. Habitat quality plays an important role in spatial dynamics when evaluating fragmented landscapes and the effectiveness of biodiversity conservation. This study aimed to evaluate the status and characteristic variation in habitat quality to analyze the underlying factors affecting habitat quality in the Guangdong–Hong Kong–Macao Greater Bay Area (GBA). Here, we applied Kendall’s rank correlation method to calculate the sensitivity of habitat types to threat factors for the Integrated Valuation of Ecosystem Services and Tradeoffs habitat quality (InVEST-HQ) model. The spatiotemporal variation in habitat quality of the GBA in the period 1995–2015 was estimated based on the InVEST-HQ model. We analyzed the characteristic habitat quality using different ecosystem classifications and at different elevation gradients. Fractional vegetation cover, the proportion of impervious surface, population distribution and gross domestic product were included as the effect factors for habitat quality. The correlation between the effect factors and habitat quality was analyzed using Pearson’s correlation tests. The results showed that the spatial pattern of habitat quality decreased from fringe areas to central areas in the GBA, that the forest ecosystem had the highest value of habitat quality, and that habitat quality increased with elevation. In the period from 1995 to 2015, habitat quality declined markedly and this could be related to vegetation loss, land use change and intensity of human activity. Built-up land expansion and forest land fragmentation were clear markers of land use change. This study has great significance as an operational approach to mitigating the tradeoff between natural environment conservation and rapid economic development.

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