PHP MySql Update Multi rows

You have overwritten variables, like $qty.

Try this:

$qty    = $_POST['qty'];
$desc   = $_POST['desc'];
$price  = $_POST['price'];
$order  = $_POST['order'];
$customer   = $_POST['customer'];

$count = count($qty);

for($i = 0; $i < $count; $i++){
    $qty1      = $qty[$i];
    $desc1     = $desc[$i];
    $price1    = $price[$i];

    $update = mysql_query("UPDATE `orders` SET `qty` = '{$qty1}', `desc` = '{$desc1}', `price` = '{$price1}' WHERE `order_id` = '{$order}';");
}

** I suggest use MySQLi or PDO extension instead of MySQL.

UPD:

There might be a possibility, that your $qty, $desc & $price may have different length. I suggest you, to modify cycle like this:

$sql = "UPDATE `orders` SET `qty` = '{$qty1}', `desc` = '{$desc1}', `price` = '{$price1}' WHERE `order_id` = '{$order}';";

$update = mysql_query($sql);

if(mysql_errno())echo PHP_EOL, mysql_error();

It might help you obtain MySQL errors.

You are overriding the $qty, $desc and $price variables in each iteration, so they will only work in the first one

    $qty    =  $_POST['qty'];
    $desc   = $_POST['desc'];
    $price  = $_POST['price'];
    $order  = $_POST['order'];
    $customer   = $_POST['customer'];

$i = 0;
$count = count($qty);

for($i=0; $i < $count; $i++){
    $currentQty      = mysql_real_escape_string($qty[$i]);
    $currentDesc     = mysql_real_escape_string($desc[$i]);
    $currentPrice    = mysql_real_escape_string($price[$i]);


    $update = mysql_query("UPDATE `orders` SET `qty` = '".$currentQty."', `desc` = '".$currentDesc."', `price` = '".$currentPrice."' WHERE `order_id` = '".$order."' ");
}

Anyway there are so much things wrong in that code. You should filter or escape your entries before sending them to mysql and all your order items will have same qty, desc and price, as you are continuously overwriting the data using the same order_id.

Use foreach instead of for, but we assume that your arrays keep synchronized indexes:

 foreach ($qty as $index => $quantity_entry){
    $update = mysql_query("UPDATE `orders` SET
              `qty` = '" . mysql_real_escape_string($quantity_entry) . "',
              `desc` = '" . mysql_real_escape_string($desc[$index]) . "',
              `price` = '" . mysql_real_escape_string($price[$index]) . "'
               WHERE `order_id` = '" . mysql_real_escape_string($order) . "' ");
}

This way you don't have to worry about non-existent indexes... PS: notice the mysql escape - which you should never skip!

check value is set or not.. And use mysqli or PDO instead of mysql to avoid sql injection

for($i=0; $i < $count; $i++){

    $qty_val      = isset($qty[$i])?$qty[$i]:'';
    $desc_val     = isset($desc[$i])?$desc[$i]:'';
    $price_val    = isset($price[$i])?$price[$i]:'';


    $update = mysql_query("UPDATE `orders` SET `qty` = '".$qty_val."', `desc` = '".$desc_val."', `price` = '".$price_val."' WHERE `order_id` = '".$order."' ");
}

You are not assuring that all three arrays have an equal length. If one doesn't insert a price or description, the item would not get send with the request (only non-empty values are sent by a browser).

You should rework the HTML output and setup a single array with multiple key-named columns, so that you only will need to iterate over one array, instead of three.

An example would be:

<input type="text" name="product[0][qty]" value="QTY_1" />
<input type="text" name="product[0][desc]" value="DESC_1" />
<input type="text" name="product[0][price]"value="PRICE_1" />

<input type="text" name="product[1][qty]" value="QTY_2" />
<input type="text" name="product[1][desc]" value="DESC_2" />
<input type="text" name="product[1][price]"value="PRICE_2" />

Iterate over the products array with foreach and additionally check, whether the columns are set:

foreach( $_POST['product'] as $inputRow )
{
    if( !isset( $inputRow['qty'] ) || !isset( $inputRow['desc'] ) || !isset( $inputRow['price'] ) )
    {
        echo 'Some input is missing; can\'t store to database';
        continue;
    }

    /* insert to DB here, but please use prepared statement or at least escape the user inputs properly! */
}