照着官网的示例，发现可以从数据库中生成migrations，但是却查不到，debug源码发现是vendor\phalcon\migrations\src\Version\ItemCollection.php中的self::TYPE_INCREMENTAL，self::TYPE_TIMESTAMPED和self::$type比较引起的，配置文件config.php中migrationsTsBased中的配置bug，官网示例配置为true,按理说应当为时间戳，但是生成的migrations却是version版本的.

‘application’ => [
        ‘logInDb’ => true,
        ‘no-auto-increment’ => true,
        ‘skip-ref-schema’ => true,
        ‘skip-foreign-checks’ => true,
        ‘migrationsDir’ => ‘db/migrations’,
       ‘migrationsTsBased’ => true, // true – Use TIMESTAMP as version name, false – use versions
        ‘exportDataFromTables’ => [
            // Tables names
            // Attention! It will export data every new migration
        ],
    ],

将上述配置改为false，就可以了。