Phytolith-occluded carbon (PhytOC) is mainly derived from the products of photosynthesis, which can be preserved in soils and sediments for hundreds-to-thousands of years due to the resilient nature of the amorphous phytolith silica. Therefore, stable and radioactive carbon (C) isotopes of phytoliths can be effectively utilized in paleoecological and archeological research. However, there still exists debate about the applicability of C isotopes of phytoliths, as a “two-pool” hypothesis to characterize PhytOC sources has been proposed, whereby a component of the PhytOC is derived from soil organic matter (SOM) absorbed through plant roots. Therefore, it is necessary to review this topic to better understand the source of PhytOC. We introduce the stable and radioactive C isotopic compositions of PhytOC, present the impacts of different extraction methods on the study of PhytOC, and discuss the implications of these factors for determining the sources of PhytOC. Based on this review, we suggest that organic matter synthesized by photosynthesis is the main source of PhytOC. However, it is important to make clear whether and how SOM-derived C present in phytoliths influence the controversial “too-old” skew and isotopic fractionation. Though the two-pool hypothesis has been proved by many researches, the carbon isotopes of phytoliths still have potential in paleoecology and archeology, because the main source is photosynthesis and many previous studies put forward the availability of these parameters. This review also shows that phytolith C isotopes may vary with different organic C compounds within phytoliths, which needs further study at the molecular scale. Different phytolith extraction methods can influence 14C dating results.