Multiple magnetic skyrmion phases add an additional degree of freedom for skyrmion‐based ultrahigh‐density spin memory devices. Extending the field to 2D van der Waals magnets is a rewarding challenge, where the realizable degree of freedoms (e.g., thickness, twist angle, and electrical gating) and high skyrmion density result in intriguing new properties and enhanced functionality. In this work, a van der Waals interface, formed by two 2D ferromagnets Cr2Ge2Te6 and Fe3GeTe2 with a Curie temperature of ≈65 and ≈205 K, respectively, hosting two groups of magnetic skyrmions, is reported. Two sets of topological Hall effect signals are observed below 6s0 K when Cr2Ge2Te6 is magnetically ordered. These two groups of skyrmions are directly imaged using magnetic force microscopy, and supported by micromagnetic simulations. Interestingly, the magnetic skyrmions persist in the heterostructure with zero applied magnetic field. The results are promising for the realization of skyrmionic devices based on van der Waals heterostructures hosting multiple skyrmion phases. Multiple groups of magnetic skyrmions add an additional degree of freedom for skyrmion‐based ultrahigh‐density memory devices. Vertical imprinting of magnetic skyrmions in 2D layered magnetic heterostructures are reported. Two sets of topological Hall effects are observed at low temperatures and these two groups of skyrmions are directly imaged using magnetic force microscopy.