Two-dimensional van der Waals (2D vdW) magnets have attracted great attention recently and possess the unprecedented advantages of incorporating high-quality vdW heterostructures and homostructures into spintronic devices, and exploring various physical phenomena or technologies. Among them, Fe₅GeTe₂ (F5GT) has ferromagnetic order close to room temperature, however the magnetic properties near its intrinsic transitions and F5GT-based 2D devices remain mostly unexplored. Here, we systematically demonstrate the peculiar magnetic properties of Fe₅GeTe₂ nanoflakes near its intrinsic transition temperature (T_p) which is far lower than its Curie temperature (T_C) of ~ 265 K, and firstly discover anomalous magnetoresistance effect in F5GT homo-junctions by magneto-transport measurements. The strongest anomalous Hall effect occurs around T_p which is located in a temperature range from 130 to 160 K for the F5GT nanoflakes with different thicknesses. Furthermore, negative magnetoresistance (N-MR) and butterfly-shaped magnetoresistance (B-MR) are observed in F5GT homo-junction devices, and they appeared only in an intermediate temperature range from 110 to 160 K, noticeably showing the maxima near the T_p rather than the lowest temperature. Our experimental results clearly reveal the significant influence of intrinsic transitions on magnetic properties of F5GT and magnetoresistance effect in F5GT homo-junction devices, which imply a new strategy to achieve high-performance 2D spintronic devices by tuning intrinsic magnetic or structural transitions in 2D vdW magnets.