Hi I want to draw a 3D graph on top of the periodic table like the picture above. Is there any program that I could just put data in or any tools that can help me to draw a graph as similar as possible?
Free LibreOffice Calc, available for most operating systems, has a 3D Look Bar Chart option. Likely, MS Word Excel has similar options.
That said, the chart in your example shows perspective, which might not be an option for free consumer products. You might ask the author what utility was used: it likely was a high-end (read "dear") publishing suite such as Adobe Illustrator.