Two-dimensional (2D) transition metal dichalcogenides (TMDs) are promising materials for numerous emergent applications. Here, we apply atomic-resolution scanning transmission electron microscopy (TEM) to resolve the intermediate stages during chemical vapor deposition (CVD) synthesis of 2D rhenium diselenide (ReSe2). Contradictory to the conventional growth models proposed previously, stable intermediate species, viz., molecular metal chalcogenide clusters, are experimentally unveiled. These molecular clusters present in the chemical vapor deposition chamber can significantly alter the growth kinetics, mass transport, and surface anchoring sites. The new layer nucleation and the formed flake morphology are both substantially influenced. Our work resolved the critical question of whether nucleation occurs in atmosphere or on the solid surface. Besides, additional experiments show that the hydrogen environment in the CVD chamber can mitigate the aggregation problem of clusters, which is decisive for obtaining uniform 2D full films. Combined with density functional theory (DFT) calculations, the key reaction steps during growth are identified. Here, we show a clear picture of the debated growth mechanisms of 2D TMDs, expected to facilitate further optimization of CVD growth conditions to achieve stable mass production.