The estimation of surface urban heat island intensity (SUHII) is crucial for studying the urban thermal environment, which is influenced not only by the commonly known definition of rural reference but also by the delineation of urban extent. Existing studies relies on various urban extent products defined in different ways, and the influence of urban extent discrepancy (UED) on SUHII estimates still remains unclear. In this study, we collected five open-source global urban extent products (GUEPs) for the year 2015 and corresponding daily land surface temperature (LST) observations (MYD11A1). Based on these products, we quantified the UED-induced uncertainty in SUHII estimates by comparing absolute difference (ΔSUHII_AD) and relative difference (ΔSUHII_RD) in SUHII among GUEPs across 892 global cities. Besides, we introduced an ISF-constrained (ISF–C) method to reduce SUHII differences among GUEPs by constraining the impervious surface fraction (ISF) within urban and rural extents. The results show that urban extents delineated by different GUEPs are not consistent, leading to their difference in ISF as well as LST, which in turn causes uncertainties in the estimated SUHII. On average for global cities, the annual daytime and nighttime ΔSUHII_AD are 0.46 ± 0.02 °C (mean ± 95% confidence interval) and 0.24 ± 0.01 °C, with corresponding ΔSUHII_RD of 42.0 ± 2.7% and 35.2 ± 2.3%, respectively. The UED-induced uncertainty in SUHII estimates varies among climate zones, and the annual daytime ΔSUHII_RD averaged for cities located in the arid zone reaches up to 60.8 ± 6.6%, which is nearly twice as high as that in other climate zones. More importantly, both ΔSUHII_AD and ΔSUHII_RD show lower values when using the ISF-C method, implying the effectiveness of this method. This study highlights the non-negligible impact of UED on the estimation of SUHII, which requires more attention due to the inconsistency of urban extents among current products.