This might be difficult to answer without more details, do you mean per capita literacy rates in each country? China's enormous population (even 200 years ago) would mean that there were both more literate and illiterate people than in Japan. Just as an example: there would have been hundreds of thousands of students in China who were literate enough to take imperial examinations.

Literacy in China was historically low. There are no real statistics on this in the premodern period, but we do know that in 1949 when the Communists took over the literacy rates was approximately 20%. So 50 years of trying to get literacy higher after 1895 did not yield great results. (Obviously Wars and Civil Wars did not help.) So my guess is that in 1800 we are talking at most 10% of the people who are literate.

http://app1.chinadaily.com.cn/star/2002/0711/cu18-1.html

In Japan we have data from 1870s and 1880s. This data shows that there's a huge variety depending on locale. Some report overall literacy rates (being able to write their own names) of 64% (Shiga prefecture where 89% of men could read and write and 39% of women could read and write in 1877 stands out), while Kagoshima prefecture report literacy rates of 18%. This is only a few years after compulsory education, so the data is the result of Edo period (1603-1868) education.

http://dspace.lib.niigata-u.ac.jp:8080/dspace/bitstream/10191/8186/1/70%284%29_524-535.pdf

p.526 of the article above has a box with the data

From this we can say that in Japan had more literate people than China 200 years ago. My guess: China's estimate is under 10%, while Japan's estimate is 40%.