The flagship phone refers to a companies best phone that it ever created till that time. Other words, flagship phone is a term used in the mobile marketing sector which means the trademark product with a latest and high-end processor, display, memory and battery. This phone will be the best model for the company at that time.
Actually, the term flagship came from the Navy. The commanding officer travelling ship is known as flagship. That ship has the most modern and advanced devices. So with this simple example can easily understand the flagship term usage. In business, the companies most efficient product or resources is known as the flagship piece.
Consider one plus, now(2019 Dec) their flagship phone is OnePlus 7 Pro. This will change from time to time. All-time companies are upgrading phones with latest technologies in both hardware and software.
Mostly, users are waiting for the flagship product to achieve maximum performance. So the company will take more care to build flagship products.