It all depends on the speaker. If one considers a company as a group of people (for example, thinking about the employees), they normally use the pronoun 'they'. If, on the other hand, one considers a company as a business and wants to refer to the business itself rather than the people working in it, they normally use the pronoun 'it'.

Both can be used, as it is a company but they are also a group of people. You can therefore use both without any difference.

Which company are you referring to?. Are we correctly assuming you mean a business? company of soldiers? you would refer to both in the same way. They/it. or are you referring to the company of friends and other people? which would be their company/the company. you could also refer to all these types of company in other ways or even mix up the references above. If we had the previous sentence we could help you​ much better and more fully.