A MNC has the head quarters in one country (home country for that company) and has operations (production, sales, services etc.) in multiple countries across the globe. A national or domestic company has all operations within a country.
A MNC has to deal with the LAWS and issues - legal, tax, import, export and labor laws - related to multiple countries. Domestic companies have to deal with one.
A MNC is generally profit oriented and can use many means to enter markets and make profits. A MNC may use a lot of funds and international pressures to establish itself in a country and throw out small competitors and even some national companies. When a MNC earns profit, the money goes out of the country. The profit goes out of the country's economy.
When a national company earns profit, the profit in invested back in the country and contributes to the development of country in some way. Many national companies can help social causes, welfare of the citizens. MNC looks mainly for profits.