<p>Habitat is one of the important contents in regional ecological security research. However, whether the impact of human activities on habitat quality has been effectively controlled remains to be further explored. Using urban–rural gradients, spatial autocorrelation analysis, and the MGWR model, we assessed how human activities have affected habitat quality in the Chengdu–Chongqing urban agglomeration. Our results show that habitat quality has consistently declined over the past two decades, exhibiting a “low in the middle, high around the edges” spatial distribution pattern. Over 60% of the area is at medium or lower habitat quality levels. Simultaneously, the human activity intensity has clearly increased, affecting approximately 114,354.68 km² of area. Although habitat quality is slowly declining and the negative effects of human activities are being gradually controlled, the areas with both low human activity and low habitat quality have grown by 42.83%, suggesting that the management of human activities is expected to face increasing challenges in the future.</p>