China has nukes, Japan doesn't. Unless you count the damage from leaking nuclear reactors.
Also, China has a large military and a young population, Japans population is aging with fewer service-aged citizens.
Both countries have all-volunteer militaries (conscripts tend to do a lot worse). But to be fair, Japan's military is much better trained (thanks to the U.S), and China's military tends to be politicized - it's similar to the U.S.S.R in WW II, in which Stalin kept interfering until Germany had taken half of Russia. At that point, he kept his hands off and let the professional fight the war, which pushed Germany back to Berlin.
Then again you'd have to consider the alliances of the area - even excluding the U.S. First Taiwan, despite disputes over ownership of the Senkaku (Tiaoyutai) islands, would side with Japan. And though Koreans tend to hate Japanese for former war atrocities (and Japan's censorship of its own guilt), Korea in general would probably ally with Japan (ironically, North Korea would provide the essential buffer keeping Korea safe from immediate retaliation from China). So between the three of them, much of China would be cut off from ocean-going world trade - including fuel and supplies.
After that it gets a bit fuzzy to predict. I think most countries would try to remain neutral initially, but woud be drawn in - particularly India, which has border disputes with China, and Russia, which distrusts China but kind of needs it to keep buying oil and resources, but also needs Europe, and is the greatest country in the world except for all its problems all caused by the United States and not corruption etc.. Add Australia, the U.S, Pakistan, etc., and you can keep yourself entertained for days predicting utterly improbably things.
But original point stands - Japan can't nuke China, despite many Japanese politicians advocating that they should be able to.