The urban–rural temperature difference is widely used in measuring surface urban heat island intensity (SUHII), where the accurate determination of rural background is crucial. However, traditionally, the entire permeable rural surface has been selected to represent the background temperature, leaving uncertainty about the impact of non-uniform rural surfaces with multiple land covers on the accuracy of SUHII quantification. In this study, we proposed two quantifications of SUHII derived from the primary (SUHII1) and secondary (SUHII2) land types, respectively, which successively occupy over 40–50% of whole rural regions. The spatial integration and temporal variation of SUHII1 and SUHII2 were compared with the result from whole rural regions (SUHII) within 34 urban agglomerations (UAs) in China. The results showed that the SUHII1 and SUHII2 differed slightly with SUHII, and the correlation coefficients of SUHII and SUHII1/SUHII2 are generally above 0.9 in most (32) UAs. Regarding the long-term SUHII between 2003 and 2019, the three methods demonstrated similar seasonal patterns, although SUHII1 (or SUHII2) tended to overestimate or underestimate compared to SUHII. As for the multi-year integration at the regional scale, the day–night cycle and monthly variations of SUHII1 and SUHII were found to be identical for each geographical division separately, indicating that the spatiotemporal pattern revealed by SUHII is minimally affected by the diversity of rural landcover types. The findings confirmed the viability of the urban–rural LST difference method for measuring long-term regional SUHII patterns under non-uniform rural land cover types.