This is a taxation method under Japan's tax system. If you are not a Japanese tax resident, a different set of tax rules will apply to your gains and dividends.
How it works
Under separate self-assessment taxation, capital gains from selling stocks and certain dividend income are taxed at an independent rate, without being combined with income such as salary. If you use a "with withholding" specific account, the brokerage automatically calculates and collects the tax under this method.
Difference from comprehensive taxation
Comprehensive taxation (see related page) combines the income with other income and applies progressive tax rates, whereas separate self-assessment taxation applies a flat rate regardless of your overall income level. Which is more advantageous depends on your situation, so please consult a qualified tax accountant.