Let the variant of the 3-SAT problem you describe be called EQUAL-3-SAT, where (following your definition) each clause has at most 3 literals. We prove EQUAL-3-SAT is NP-complete by a reduction from 3-SAT as follows.
Let $\phi$ be an instance of 3-SAT with $n$ variables and $m$ clauses. If $\phi$ is balanced already in the beginning (the case $n=m$), we do nothing. If $n > m$, we introduce a fresh variable $x$ that does not appear anywhere in $\phi$ and add to $\phi$ exactly $n-m+1$ clauses of the form $(x)$, so we have $n=m$, and we are done.
Then, if $n < m$, we can do similar balancing: each addition of a 3-literal clause $(a \vee b \vee c)$, where $a$, $b$ and $c$ are fresh variables, increases $n$ by $3$, and $m$ by $1$. Keep adding this clause to $\phi$ until $n=m$, or the difference between $n$ and $m$ is exactly one or three (if the difference was two, repeating the process once more would balance $\phi$). If the difference is one, adding one more 3-literal clause causes $n=m+1$ thus we use the balancing process of the first step (case $n > m$). If the difference is three, we simply add an 2-clause of the form $(a \vee b)$, increasing $n$ by two and $m$ by one, again giving us $n=m$.
Finally, we observe the new formula is satisfiable if and only if $\phi$ was.