select * from table1 join table2 on table1.column3=table2.column4 where ...
...
$row=mysql_fetch_assoc($result);
However, there are two columns in the new table(table1 join table2) which have the same column name, how to get the values of both respectively?
Call the columsn out specifically with an alias like
SELECT table_1.id as table_1_id, table_2.id as table_2_idYoull have to list out all or most of the columns form at least one of the tables this way but you can get access to cols with the same name across multiple tables.