You're almost there:

• Not sure that you need the array calc if your aim is to print the table
• Define a new variable row inside the outer loop as an empty array, [];
• In the inner loop, instead of calc.push, use row.push
• After the inner loop, you have a complete row, which you can output using the array .join() method
• If you need to, then add the row to calc with calc.push(row); not necessary in my view.

const n = 3;
//const calc = []; //may not be necessary

for (let i = 1; i <= n; i++) {
    const row = [];
    for (let j = 1; j <= n; j++) {
        row.push(i + " x " + j + " = " + (i * j));
    }
    console.log( row.join(' | ') );
    //calc.push(row);//not sure if you still need this
}
/* OUTPUT
1 x 1 = 1 | 1 x 2 = 2 | 1 x 3 = 3
2 x 1 = 2 | 2 x 2 = 4 | 2 x 3 = 6
3 x 1 = 3 | 3 x 2 = 6 | 3 x 3 = 9
*/

From the code you've presented, it appears that you're yet to understand what a 2d array really is. The way you've done it, everything's just stuffed into a single 1d array.

You may think of the pixels on a screen as being part of a 2d array. The first array holds all of the horizontal lines. The horizontal lines contain the pixels.

So.. let's concentrate on that part first.

let result = [];

for (var y=0; y<n; y++)
{
    result.push( [] );
    for (var x=0; x<n; x++)
    {
        result[y].push( (x+1) * (y+1) );
    }
}

First we create a result array, and then for every row in our table, we add an array that will hold the columns, then for each column in that row, we add the values.

Next, we just step through that table and turn the values into the original equations. We start by ascertaining the dimensions of the array, before we create a table the same size.

function printTable( tbl )
{
    let nRows = tbl.length;
    let nCols = tbl[0].length;
    
    for (var y=0; y<nRows; y++)
    {
        let rowStr = '';
        
        for (var x=0; x<nCols; x++)
        {
            if (x!=0) rowStr += " | ";
            rowStr += `${y+1} x ${x+1} = ${tbl[y][x]}`;
        }
        console.log(rowStr);
    }
}

Chucking it all together, I present the following code. Yes, I know you're not using functions yet - but you can still see the important concepts. You can change it so that the whole equation for each entry in the table is saved, instead of just the answer.

window.addEventListener('load', init, false);

function init()
{
    let result = makeMultTable(3);
    printTable(result);
}

function makeMultTable(n)
{
    let result = [];
    
    for (var y=0; y<n; y++)
    {
        result.push( [] );
        for (var x=0; x<n; x++)
        {
            result[y].push( (x+1) * (y+1) );
        }
    }
    return result;
}

function printTable( tbl )
{
    let nRows = tbl.length;
    let nCols = tbl[0].length;
    
    for (var y=0; y<nRows; y++)
    {
        let rowStr = '';
        
        for (var x=0; x<nCols; x++)
        {
            if (x!=0) rowStr += " | ";
            rowStr += `${y+1} x ${x+1} = ${tbl[y][x]}`;
        }
        console.log(rowStr);
    }
}

Multiplication of table in two dimension array

Function name: multiplyNumber

Syntex multiplyNumber(n)

• n Number to be passed to function to create table upto that number.

Snippet

function multiplyNumber(n){
        let table  = [];
        let data = [];
        for (var i = 1; i <= n; i++){
                for (var j = 1; j <= n; j++){
                        data.push(`${i} x ${j} = ${i * j}`);
                }
        table.push(data); // pushing data to table.
        data = []; //Resetting data array to store new data each time.
        }
        return table;
}

var result = multiplyNumber(3);
console.log(result);