They say it follows from above mentioned theorem that the structure $(\mathbb{R}, +, \times, 0,1)$ has a countable model which is super-counterintuitive since $\mathbb{R}$ has uncountably many numbers, so how can a model be countable there? Can one give one example that shows how a countable model could come from a structure with uncountable many elements?
I mean in above structure there are truths like "$1+1=2$", "$0.5 \times 0.5 = 0.25$" etc., right? These are easily uncountably many truths = uncountable model. So how is it possible to reduce this uncountable model to a countable model without manipulating the structure?
You ask for an example. Let $R = \overline{\mathbb{Q}}\cap \mathbb{R} = \{r\in \mathbb{R}\mid r\text{ is algebraic over }\mathbb{Q}\}$ be the set of real algebraic numbers. Then $R$ is countable, and $(R,+,\times,0,1)$ is a model of the complete theory of $\mathbb{R}$.
This is not easy to see directly, but it follows from the fact that the complete theory of $\mathbb{R}$ is axiomatized by the axioms of real closed fields, and $R$ is a real closed field.
Your question suggests that you have serious misunderstandings about the meanings of "theory" and "model". To start, you write
This is nonsense. Structures don't have models, theories do. What the Löwenheim-Skolem theorem says is that every theory in a countable language which has an infinite model has a countably infinite model. So what we can conclude is $\text{Th}(\mathbb{R})$, the set of all sentences in the language $\{+,\times,0,1\}$ true in $\mathbb{R}$, has a countable model.
There would be uncountably many truths (sentences in $\text{Th}(\mathbb{R})$) if we could talk about arbitrary real numbers in our sentences. But we can't: we're restricted to using the symbols $+,\times,0,1$. There are only countably many formulas in the language, so there are only countably many truths in $\text{Th}(\mathbb{R})$.
Now you could expand the language to include a constant symbol naming every element of $\mathbb{R}$. Then the language would be uncountable, and the Löwenheim-Skolem theorem would fail to give us a countable model.
I have no idea what "without manipulating the structure" means.