Hardware ( QNAP hardware is better than Synology )
QNAP has more than 140 models available today, while Synology only has 45+. QNAP's hardware spec selection is staggering - there's a NAS for every processor (there's one that's even powered by a ZhaoXin processor - yes, that exists).
Not only are there more models offered in QNAP , but there are some features that only QNAP NAS offers, such as Thunderbolt ports on some units, FC card connectivity, HDMI port, etc. There are QNAP models that even have 2.5" and 3.5" bays in the same unit.
Firmware Security ( Synology has a more secure firmware )
Both QNAP and Synology work with very similar Linux based firmware. The look, feel and functionality of these devices are very similar BUT there is a difference.QNPA tends to have more apps - both QNAP's own apps and third-party apps. This also means that there are outdated and even less secure apps on QNAP.
Synology has fewer apps, but most of them are stable. UI Synology DSM is cleaner than QNAP QTS
Both Synology and QNAP (on select models) offer Docker, so you can install containerized apps.
Recently, more QNAPs have been affected by Deadbolt than Synology. So Synology DSM and applications are both more secure than QNAP.
Hard drive compatibility (QNAP has an open drive model, certain Synology models lock you into their drives).
Certain Synology models only allow the use of Synology branded drives. The list of qualified drives does not include any brand other than Synology for such models. Synology branded hard drives are based on Toshiba MG with special firmware and are usually more expensive than Toshiba MG, Ultrastar or Exos. Synology claims that their hard drives offer 23% better performance, so it is not a bad idea to buy Synology with their hard drives, but you are locked on such models with THEIR drives.QNAP's list of qualified drives, on the other hand, includes all brands. So QNAP has a more open policy towards third-party drives and QNAP is the winner in this scenario.
Data Protection ( Almost a draw with a slight advantage for Synology )
Both vendors offer similar data backups such as RAID, pool, snapshots, remote replication, private cloud capability and remote public cloud backup. They are both equally good in this regard.Qnap uses ZFS on the higher models and EXT on the lower models, while Synology uses BTRFS or EXT and this does not affect data protection.
Synology is able to offer high availability clusters even in the small devices, which QNAP cannot, so Synology is slightly better here.
Frequency of operating system updates (tie)
Since both QNAP and Synology are Linux-based, their OS major versions are released whenever a new Linux LTS kernel comes out. So the frequency of major releases OS is the same for both. Both are also equally proactive with minor releases.