A search for long-range magnetic ordering in two-dimensional materials is recently providing a huge platform for the study of spin-related phenomena. However, the ferromagnetic order of FenGeTe2 (n = 3, 4, 5) still shows ambiguities and needs to be clarified. Here we report the thickness- and temperature-dependent anomalous Hall effects in h-BN/Fe3GeTe2/SiO2 van der Waals heterostructures with the thickness range of 28–175 layers of Fe3GeTe2. The anomalous Hall effects in thinner Fe3GeTe2 flakes show a square-shaped Hall signal with a strong perpendicular magnetic anisotropy, whereas bulk flakes show a gradual switching with the magnetic field due to the presence of multi- or labyrinthine domain structures, consistent with earlier reports. A surprising non-monotonic variation of the anomalous Hall remanence and saturation values with temperatures is observed to indicate a phase transition around 110–125 K, which could be due to a possible formation of an antiferromagnetic state at lower temperatures in Fe3GeTe2. Such an antiferromagnetic transition can be explained in a coupled picture of itinerant electrons and local magnetic moments in relation to the Kondo screening. An additional transition at 150–160 K is also observed in the remanence and the resistance, implying a more complicated mechanism playing a role in the magnetic phases of Fe3GeTe2. A persistence of the anomalous Hall effects observed above the Curie temperature where the remanence disappears further supports the interplay of the itinerant electrons and the local moments.