Satellite-based vegetation datasets enable vegetation phenology detection at large scales, among which Solar-Induced Chlorophyll Fluorescence (SIF) and Enhanced Vegetation Index (EVI) are widely used proxies for detecting phenology from photosynthesis and greenness perspectives, respectively. Recent studies have revealed the divergent performances of SIF and EVI for estimating different phenology metrics, i.e., the start of season (SOS) and the end of season (EOS); however, the underlying mechanisms are unclear. In this study, we compared the SOS and EOS of natural ecosystems derived from SIF and EVI in China and explored the underlying mechanisms by investigating the relationships between the differences of phenology derived from SIF and EVI and climatic limiting factors (i.e., temperature, water and radiation). The results showed that the differences between phenology generated using SIF and EVI were diverse in space, which had a close relationship with climatic limitations. The increasing climatic limitation index could result in larger differences in phenology from SIF and EVI for each dominant climate-limited area. The phenology extracted using SIF was more correlated with climatic limiting factors than that using EVI, especially in water-limited areas, making it the main cause of the difference in phenology from SIF and EVI. These findings highlight the impact of climatic limitation on the differences of phenology from SIF and EVI and improve our understanding of land surface phenology from greenness and photosynthesis perspectives.