"Livability" is at the core of building a high-quality living circle in the Guangdong-Hong Kong-Macao Greater Bay Area (GHMGBA), and the excessive housing burden costs have become an important obstacle to livability. The differentiation of the rental market is an indispensable and important part of the housing market in the GHMGBA and is inseparable from the creation of a livable life circle. Based on the average housing rent of 58 counties in the GHMGBA, this study summarizes the patterns and characteristics of the spatial differences in housing rents through the construction of a “grading pyramid of housing rents”, and displays the spatial pattern of housing rents through spatial autocorrelation analysis, cross-border rent gap comparison, and price-to-rent ratio analysis. From the theoretical perspective of leasing demand and urban fundamentals, this study constructs a model of factors influencing rent differences, consisting of population growth, per capita housing area, income level, economic level, industrial structure, and education structure. Through model comparison, a spatial lag model was used to measure the main factors influencing the housing rents in the GHMGBA. Based on the geographical detector, the study further analyzed the differences in the intensity of the factors' influence. The results showed that the housing rents in the GHMGBA generally presented a two-level difference pattern. The pattern was dominated by domestic and foreign differences between Hong Kong, Macao, and nine cities in the Pearl River Delta, as well as the differences between the core areas of Guangzhou, Shenzhen, and other regions. The cross-border rent difference was the highest. Higher price-to-rent ratios were observed in Guangzhou, Shenzhen, and Zhuhai. Income level, economic level, per capita housing area, and industrial structure had a significant impact on housing rent differences in the GHMGBA. Among them, income level had the highest impact intensity. This study responds to cross-border regional differences within the country from the perspective of housing rent. Cross-border differences are not only reflected in the population′s economic, income, and institutional levels, but also in the housing rent. The key issue for the regional linkage development of the housing market in the GHMGBA and the construction of a livable and quality living area is the coordinated development across borders.