It's said that the primitive concepts of set theory are those of "set" and "membership", then all axioms of set theory must begin with "Let $A$ be a set" or "Let $x\in A$", but they don't. For example, let us consider the subset axiom:
Subset Axiom. Let $\varphi(x)$ be a formula and let $A$ be a set. Then there exists a set $S$ such that for all sets $x$ we have that $x\in S$ if and only if $x\in A$ and $\varphi(x)$.
This axiom begins with "Let $\varphi(x)$ be a formula" but "formula" is not a primitive concept, then, for having sense, it must be a defined concept, but as far as I see we can't define "formula" in terms of "set" and "membership" if I am wrong, please tell me. Now, in the case where we can't define "formula", how is the subset axiom justified from a logical point of view?
In many books, when the subset axioms is introduced, the statement "Let $\varphi(x)$" is used informally, I will appreciate if you recommend me a book on set theory where the concept of "formula" is used formally, where there is a formal definition of what a formula is.
Thank you for your reading.
In formalizations of set theory (e.g. ZFC), this subset axiom you've described in usually called the axiom schema of specification. Note the use of the word "schema" in its name: this is where your confusion stems from. Indeed, formally speaking, this is not a single axiom, but a whole collection of axioms: one for every formula $\phi(x)$. For every formula $\phi(x)$, there is an axiom of set theory which goes "$\forall A \exists S \forall x (x \in S \Leftrightarrow (x \in A \wedge \phi(x)))$". Taken together, all these axioms make up what you call the subset axiom.
Edit: Axiomatic set theory is based on first-order logic, which is the system of language and inferences that are used to do this sort of math. It starts with symbols (including variables, connectives like $\neg$ and $\wedge$, quantifiers $\forall$ and $\exists$, the $=$ symbol, and predicate symbols) which are combined according to certain rules to make formulas. First-order logic also uses rules of inference to deduce some formulas from others. Set theory uses first-order logic with the predicate symbol $\in$; its axioms and theorems are formulas. I suggest reading some more (on Wikipedia or in your favorite textbook) if you're interested in learning more about how first-order logic works.