The urban heat island (UHI) effect, in which urbanized areas tend to have warmer conditions compared to their rural surroundings, has drawn increasing attention in recent years. Using ground-based and satellite remote sensing data, we present a method to quantify the spatial pattern and diurnal and seasonal variations in canopy layer heat islands (CLHIs) in China`s 32 major cities during 2009 and investigate their relationships with built-up intensity (BI), nighttime lights, vegetation activity, surface albedo, and surface urban heat island intensity (SUHII). The results show that both the annual daytime and nighttime CLHI intensities (CLHIIs) were positive ranging from 0.2 °C to 2.2 °C and from 0.3 °C to 2.4 °C for these major cities, respectively. Higher CLHIIs were observed in the night, especially for northern parts of China. Along urban-rural gradients, the CLHI effect had an exponential decay shape and differed greatly by season. The CLHII distribution correlated positively and significantly to BI and nighttime lights. Vegetation activity was negatively correlated with the CLHII and more strongly in summer. Surface albedo showed an extremely weak correlation with the CLHII. In addition, CLHII had a strong correlation with SUHII. The annual daytime SUHII was 1.2 ± 1.1 °C (mean ± standard deviation) with 0.40 °C (95% confidence interval 0.36 to 0.44 °C) of annual daytime CLHII. The annual nighttime SUHII was 2.0 ± 0.8 °C with 1.04 °C (0.99 to 1.09 °C) of annual nighttime CLHII. Our results suggest that, reducing built-up intensity and anthropogenic heat emissions and increasing urban vegetation provide a co-benefit of mitigating SUHI and CLHI effects.