For example the shape of a fighter jet compared to a boeing 747.
as it is said in the comment, there is no short answer for this one.
If we just focus on the Aerodynamics, there are some important differences between the approach used in commercial and military aircrafts when designing an aircraft. I believe the most relevant are the following.
Firstly, commercial planes are designed for an optimal cruise condition in order to reduce fuel consumption. This is function of the Mach, the performance of the engine and the aerodynamics of the plane. On the other hand, for a fighter as the one you mention, good performance has to be achieved for an entire envelope, including subsonic-supersonic regimes and different altitudes. This will determine characteristics like the shape of the wing and fuselage itself, engines (very important to take into account for the aerodynamics as well)...
Secondly, in terms of stability, you will find opposite approaches. It is very important to understand that one always has to sacrifice stability in order to achieve some levels of manoeuvrability. A commercial plane aims to achieve high levels of longitudinal and lateral stability; whereas a fighter needs to be able to perform way more demanding manoeuvres and is inherently unstable. This will of course be an important part when designing a fighter and set the aerodynamic centre of pressure (size of lifting surfaces, fuselage, use of configurations such as a canard…).
Again, these are some factors that are taken into account, however I hope this helps to understand some of the differences from the aerodynamics point of view.