The present invention discloses a colorful board structure comprising a transparent substrate, an adhesive layer, a three-dimensional painted layer and a protective layer. The three-dimensional painted layer includes at least one colored layer and at least one transparent stacking layer including at least one raised part. The aforementioned colorful board structure is made of a multi-layer structure, and has the advantages of enhancing the stereoscopic effect of the pattern and the color expression. In addition, a manufacturing method of the colorful board structure is also disclosed.