The basic A-series planes were armed with two 7.92 mm MG 17 and two 20 mm MG 151/20 in the nose and delivered as the Me 410 A-1 light bomber. The originally planned heavy fighter Me 410 A-2 was cancelled because the dual MK 103 cannon pack was not ready in time. The Me 410A featured a bomb bay for carrying air-to-ground ordnance or for the installation of additional air-to-air weaponry or other equipment. Initially, three Umrüst-Bausätze (conversion kits) were available, U1 contained a palette of cameras for the photo-reconnaissance role, U2 two 20mm MG 151/20 cannon with 250 rounds each for the heavy fighter use, and U4 used the 50 mm BK5 cannon with 21 rounds to turn the aircraft into a dedicated bomber destroyer. The BK5 cannon, derived from a now outdated anti-tank weapon, allowed the 410s to shoot at their targets from over 1,000 yards, a distance at which the bombers' guns were useless for defense. The low rate of fire and limited ammunition supply together with the extra weight of the large gun made the other anti-bomber versions of Me 410, especially those with extra MG 151/20 cannon, much more useful. The dedicated reconnaissance version Me 410 A-3 received a deeper fuselage for additional cameras and fuel. The 410 A-3 entered service in small numbers in early 1944, and equipped three long-range reconnaissance Staffeln (one on the Western Front and the other two on the Eastern Front).
The Me 410B-series was largely the same as the A-series, but replaced the 7.92 mm MG 17's with 13 mm MG 131. The originally planned 1,900 hp (1.397 kW) DB 603G engine was cancelled in early 1944 so all 410B's used DB 603A or DB 603AA engines, just like the A-series. The DB 603G would have increased the maximum speed to 630 km/h (392 mph), and cruising speed to 595 km/h (370 mph), although the weights increased once again. The versions were the same as with the A-series, the Me 410 B-1, Me 410 B-2 and Me 410 B-3 filling the same roles as the earlier A-1, A-2 and A-3 versions.
Several experimental models were also developed. The Me 410 B-5 added shackles under the fuselage to carry a torpedo, and removed the MG 131s in the nose to make room for the FuG 200 Hohentwiel ship-search radar. The bomb bay was not used in this version in order to make room for a 650 litre fuel tank, and the defensive gun barbettes were replaced by another 700 litre fuel tank for long-range missions. The Me 410 B-6 was a similar anti-shipping conversion, but intended for the short-range coastal role only. For this mission it did not use a torpedo, and was instead a simple modification of the B-1 with the FuG 200 radar. The Me 410 B-7/B-8 were updated B-3 reconnaissance modell that were only built as prototypes.
The Me 410C was a high-altitude version drawn up in early 1944, with two new wings designs that increased span to 18.25 m or 20.45 m (60 ft or 67 ft). The larger wings allowed the gear to retract directly to the rear. A new universal engine mount would allow for the use of any of the DB 603JZ or BMW 801J turbocharged engines or the Jumo 213E two-stage mechanically supercharged engines, driving a new four-bladed propeller with very wide blades. The 801 was air-cooled and the 213 used an annular radiator in the nose, so the normal under-wing radiators were removed and the DB powered versions would use the radiator from the 213's. None were ever built, as Me 410 production was canceled before the engines matured.
The Me 410D was a simpler upgrade to the B-series to improve altitude performance, but not to the same degree as the C-series. It would be powered by the DB 603JZ engines, and had a revised forward fuselage to increase the field of view of the pilot and reduce drag. It also replaced portions of the outer wing panels with ones made of wood to conserve strategic materials. Several were built, but like many other attempts at wood construction, the loss of the Tegofilm factory in a bombing raid meant the adhesives available were not strong enough, and the wooden portions failed.
Production was eventually canceled to concentrate on Messerschmitt Bf 109Gs in August 1944, after 1,160 Me 410s had been built.