Not sure it is the "best", but I think simulation is useful for modeling and optimizing complicated systems like supply chains in which you often find words like stochastic, uncerainty, dynamic, and so on.

SCOR Model can be a good start...

Also, game theory solutions(such as cooperative ...) can improve total profit of supply chain(or a specific supply channel).

You need to find what is the real problem, when you know wich is you know wath is the perfect method

Well, what do you want to opimise? What do you want to achieve? Being quick or cheap? Spend time defining your problem before looking for a solution.

As an aside, if you haven't done so yet, read "The Goal" - it is quite entertaining. And makes you think about how you organise your operations.

Adding to the above I would share real time information sharing to avoid bullwhip effect

Looking for optimisation at operational, tactical, strategical level?

I don't know if you already answered your question.

I could suggest to you looking for Multi-Echelon Inventory Optimization literature and practices (MEIO).

It could be enlightening.

Regards

Flavio

There are various method for optimizing the supply chain. But the most commonly used methods are mathematical models and simulation. Some authors consider the simulation models for the optimization as the most successful models in the area of the supply chain.