你那个 A 表的 id 是 主键, 并且 AUTO_INCREMENT 的么?
如果是的话, 修改 SQL 为
REPLACE INTO A (id, item, sku, data)
SELECT
A.id, main.item, main.sku, main.data
FROM
B main JOIN A
ON (main.item = A.item)
WHERE
NOT EXISTS (
SELECT 1
FROM B sub
WHERE main.item = sub.item
AND main.`time` REPLACE INTO A (id, item, sku, data)
-> SELECT
-> A.id, main.item, main.sku, main.data
-> FROM
-> B main JOIN A
-> ON (main.item = A.item)
-> WHERE
-> NOT EXISTS (
-> SELECT 1
-> FROM B sub
-> WHERE main.item = sub.item
-> AND main.`time` select * from a;
+----+------+------+------+
| id | item | sku | data |
+----+------+------+------+
| 1 | A | A | Xa |
| 3 | C | C2 | Xc |
| 5 | E | NULL | NULL |
+----+------+------+------+
3 rows in set (0.00 sec)