Two-dimensional (2D) van der Waals (vdW) materials show a range of profound physical properties that can be tailored through their incorporation in heterostructures and manipulated with external forces. The recent discovery of long-range ferromagnetic order down to atomic layers provides an additional degree of freedom in engineering 2D materials and their heterostructure devices for spintronics, valleytronics and magnetic tunnel junction switches. Here, using direct imaging by cryo-Lorentz transmission electron microscopy we show that topologically nontrivial magnetic-spin states, skyrmionic bubbles, can be realized in exfoliated insulating 2D vdW Cr2Ge2Te6. Due to the competition between dipolar interactions and uniaxial magnetic anisotropy, hexagonally-packed nanoscale bubble lattices emerge by field cooling with magnetic field applied along the out-of-plane direction. Despite a range of topological spin textures in stripe domains arising due to pair formation and annihilation of Bloch lines, bubble lattices with single chirality are prevalent. Our observation of topologically-nontrivial homochiral skyrmionic bubbles in exfoliated vdW materials provides a new avenue for novel quantum states in atomically-thin insulators for magneto-electronic and quantum devices.