Field-free room-temperature modulating magnetic domain structures and realizing stable nanoscale magnetic bubbles in 2D van der Waals (vdW) intrinsic ferromagnets are fundamentally important for 2D spintronic devices. However, it is still very challenging for the absence of a proper room-temperature 2D vdW ferromagnet with suitable perpendicular magnetic anisotropy. Here, by using a 2D vdW intrinsic room-temperature ferromagnetic Fe3GaTe2 crystal with Curie temperature of over ∼340 K and large perpendicular magnetic anisotropy, we study field-free thickness-dependent magnetic domain structure evolution in Au-capped 2D Fe3GaTe2 nanosheets by magnetic force microscopy at room temperature. The magnetic domain varies from a labyrinth-like stripe domain to a single domain in Au/Fe3GaTe2 (20/x nm) with decreasing Fe3GaTe2 thickness from 129 to 17.8 nm. Importantly, the field-free, spontaneous, stable, nanoscale magnetic bubbles can be realized in Au/Fe3GaTe2 (8/x nm) with a wide range of Fe3GaTe2 thickness over 30 nm. The highest bubble density and smallest diameter are measured as ∼2.65 μm−1 and ∼130 nm, respectively, superior to that of most room-temperature magnetic bubble materials. This work paves the way for field-free, room-temperature magnetic domain modulation and vdW-integrated spintronic applications of 2D vdW crystals.