Many-to-many Mapping table

Remarks#

Lack of an AUTO_INCREMENT id for this table — The PK given is the ‘natural’ PK; there is no good reason for a surrogate.
MEDIUMINT — This is a reminder that all INTs should be made as small as is safe (smaller ⇒ faster). Of course the declaration here must match the definition in the table being linked to.
UNSIGNED — Nearly all INTs may as well be declared non-negative
NOT NULL — Well, that’s true, isn’t it?
InnoDB — More effecient than MyISAM because of the way the PRIMARY KEY is clustered with the data in InnoDB.
INDEX(y_id, x_id) — The PRIMARY KEY makes it efficient to go one direction; the makes the other direction efficient. No need to say UNIQUE; that would be extra effort on INSERTs.
In the secondary index, saying just INDEX(y_id) would work because it would implicit include x_id. But I would rather make it more obvious that I am hoping for a ‘covering’ index.

You may want to add more columns to the table; this is rare. The extra columns could provide information about the relationship that the table represents.

You may want to add FOREIGN KEY constraints.

Typical schema

CREATE TABLE XtoY (
    # No surrogate id for this table
    x_id MEDIUMINT UNSIGNED NOT NULL,   -- For JOINing to one table
    y_id MEDIUMINT UNSIGNED NOT NULL,   -- For JOINing to the other table
    # Include other fields specific to the 'relation'
    PRIMARY KEY(x_id, y_id),            -- When starting with X
    INDEX      (y_id, x_id)             -- When starting with Y
) ENGINE=InnoDB;

(See Remarks, below, for rationale.)