12. Answer 76.

Let $|S| \geqslant 3, p_{1}^{\alpha_{1}} p_{2}^{\alpha_{2}} p_{3}^{a_{3}} \in S, p_{1}, p_{2}, p_{3}$ be three different primes, $p_{1}1, (c_{3}, c_{2})>1$.
From $(c_{1}, c_{2})=1$ we know the product of the smallest prime factors of $c_{1}, c_{2} \leqslant c_{3} \leqslant 108$. Thus $q \mid c_{1}$.
From $(c_{2}, c_{1})=1, (c_{2}, p_{1}^{\alpha_{1}} p_{2}^{\alpha_{2}} p_{3}^{a_{3}})=1, \{p_{1}, p_{2}, p_{3}, q\}=\{2,3,5,7\}, c_{2} \leqslant 108$ we know $c_{2}$ is a prime number greater than 10.
From $(c_{3}, c_{2})>1$ we know $c_{2} \mid c_{3}$. Also, $11, (c_{5}, c_{4})>1$. So $c_{2} \mid c_{5}, c_{4} \mid c_{5}$.
From $c_{2} \mid c_{3}, (c_{4}, c_{3})=1$ we know $(c_{2}, c_{4})=1$. Thus $c_{2} c_{4} \mid c_{5}$. But $c_{2} c_{4} \geqslant 11 \times 13 > 108$, a contradiction.
Take $S_{1}=\{1,2, \cdots, 108\} / (\{1\}$ and primes greater than 11 $\} \cup \{2 \times 3 \times 11, 2 \times 3 \times 5, 2^{2} \times 3 \times 5, 2 \times 3^{2} \times 5, 2 \times 3 \times 7, 2^{2} \times 3 \times 7, 2 \times 5 \times 7, 3 \times 5 \times 7\})$. Then $|S_{1}|=76$.
Below we prove that $S_{1}$ satisfies (i), (ii).
If $p_{1}^{\alpha_{1}} p_{2}^{\alpha_{2}} p_{3}^{\alpha_{3}} \in S_{1}, p_{1}1, (2 q_{1}, b)>1$; if $b \neq 3 q_{1}$, then $3 q_{1} \in S_{1}, (3 q_{1}, a)>1$, $(3 q_{1}, b)>1$.
(2) $a=2 \times 3 \times 17, b \neq a$, same as (1).
(3) $a=b$, since at least one of $5,7,11$ does not divide $a$, (i) holds.
If $a$ is composite, take the smallest prime factor $p$ of $a$, then $p \in S_{1}, (p, a)>1$; if $a$ is prime, then $a \leqslant 11$, $2a \in S_{1}, (2a, a)>1$.
(4) $a, b$ are two different numbers in $S_{1}$, $a, b$ each contain at most two different prime factors, $a1, (b, r_{1})>1$;
If $r_{1}=r_{2}=a$, then take $u=2$ or 3, such that $b \neq u a$. Then $u a \in S, (u a, a)>1, (u a, b)>1$.
If $r_{1} r_{2} \neq a, r_{1} r_{2} \neq b$, then $r_{1} r_{2} \in S_{1}, (r_{1} r_{2}, a)>1, (r_{1} r_{2}, b)>1$.
If $r_{1} r_{2}=a$, then take $u=2$ or 3, such that $b \neq u r_{1}$. Then $u r_{1} \in S, (u r_{1}, a)>1, (u r_{1}, b)>1$.
If $r_{1} r_{2}=b$, then take $v=2,3,5$, such that $a \neq u r_{1}, b \neq u r_{1}$, then $v r_{1} \in S_{1}, (v r_{1}, a)>1, (v r_{1}, b)>1$.
Therefore, $2 \times 3 \times 5, 2^{2} \times 3 \times 5, 2 \times 3^{2} \times 5, 2 \times 3 \times 7, 2^{2} \times 3 \times 7, 2 \times 5 \times 7, 3 \times 5 \times 7$ do not belong to
$S$.
Now we prove: $2 \times 3 \times 11, 2 \times 3 \times 13, 5 \times 7, 7 \cdots$ (2) do not belong to $S$.
Assume (2) numbers all belong to $S$. From (i) we know there exist $d_{1}, d_{2} \in S$, such that $(2 \times 3 \times 11, d_{1})=1, (5 \times 7, d_{1})=1$, $(2 \times 3 \times 13, d_{2})=1, (5 \times 7, d_{2})=1$.

Thus $d_{1}, d_{2}$ are both primes greater than 10. From (ii) we know $d_{1}=d_{2} \geqslant 17$. From (ii) we know there exists $d_{3} \in S$, such that $(7, d_{3})>1, (d_{2}, d_{3})>1$.
Thus, $7 d_{2} \mid d_{3}$. But $7 d_{2} \geqslant 7 \times 17=119$, a contradiction.
On the other hand, among the primes greater than 10, at most one belongs to $S, 1 \notin S$, thus $|S| \leqslant 108-7-1-23-1 = 76$.