To put it simply, China wasn't conquered by Japan.

First of all Japan isn't small. Its larger than the whole of Germany and had a considerably larger population than the European superpowers' various native homeland numbers. Its almost the total of Germany's mainland population during the war.

China as a nation still only existed on paper.In reality a lot of ethnic, racial,religious, and political divisions meant in practise it was actually multiple countries in one large drawn border. And than even within the main place we can call China, there was a civil war between communists and the federal government.

This is not counting how the National government had a poorly trained army while the Japanese army was among the top tier armies of the world hence the impression China was weak. When we see the communists and ethnic groups of other regions such as Muslims tribes fight the Japanese, the results were far more even and the Japanese often could not expand beyond the main Federal territory (not to mentioned the Nationalists bogged them down).

The best answer is that Japan was a superpower the Nationalist government poorly prepared for war but had plenty of problems in China that balanced it out from terrain to multiple factions as enemies in addition to the Nationalist and supplyline issues because of the size of China and China's poorly developed infrastructure (and how harsh the terrain was to travel over).

Both sides had too much problems that Japan's great gap in military power was not enough to defeat the Chinese.