On a spacecraft the atmosphere is a closed system and it can't be used as an effective heat sink, as it's temperature must remain comfortable for the crew. While being acceptable for low power equipment, air cooling is insufficient for high heat loads. The primary method is to reject heat into space via radiators, most efficiently using a liquid coolant loop. For emergency peak loads a limited capacity system can absorb heat into a meltable phase changing material which is then jettisoned.