使用案例

SELECT 
  SUM(case when  t2.Flag = t1.Code then 1 else 0 end) AS TRUE_CNT, 
  SUM(case when t1.Code is not null and t2.Flag <> t1.Code then 1 else 0 end) AS FALSE_CNT,  
  SUM(case when  t1.Code IS NULL then 1 else 0 end) AS  NULL_CNT
FROM Table2 AS t2 
LEFT JOIN Table1 AS t1 ON t2.Merchant_ID = t1.ID

做一个 Left join 从表2到表1使用 ID .
使用聚合函数，如 Sum() ，具有条件函数/运算符，如 Ifnull() , IS NOT NULL . Code 是mysql中的关键字。您应该避免将其用作表名，而是使用其他名称。如果您仍然需要使用它，您将不得不在它周围使用反记号。
尝试以下操作（db fiddle演示）：

SELECT 
  SUM(IF(t1.`Code` IS NOT NULL, t2.Flag = t1.`Code`, 0)) AS `TRUE`, 
  SUM(IF(t1.`Code` IS NOT NULL, t2.Flag <> t1.`Code`, 0)) AS `FALSE`, 
  SUM(IF(t1.`Code` IS NULL, 1, 0)) AS `NULL`
FROM Table2 AS t2 
LEFT JOIN Table1 AS t1 ON t1.ID = t2.Merchant_ID

缩短版（db fiddle）：

SELECT 
  SUM(t1.`Code` IS NOT NULL AND t2.Flag = t1.`Code`) AS `TRUE`, 
  SUM(t1.`Code` IS NOT NULL AND t2.Flag <> t1.`Code`) AS `FALSE`,  
  SUM(t1.`Code` IS NULL) AS `NULL`
FROM Table2 AS t2 
LEFT JOIN Table1 AS t1 ON t1.ID = t2.Merchant_ID;