Can I apply for a Japanese visa directly with my China passport in Singapore?

There is no visa-free visa for China passport and no transit visa.

Therefore, as long as it is a China passport, no matter which country the visa is, you must apply for a visa before you can go to Singapore.

It's cheaper to go to the Singapore consulate, but going in person may not be suitable for you. You can find a travel agency to do it. For students, a scanned copy of the study certificate or student ID card, a scanned copy of the whole page of the household registration book, and then the first page of the passport and the scanned page of the photo will be enough. And if the travel agency wants to do it, send an email to them. After a PDF file is completed, it will be a visa, and it will be ok to send it to you.