A nucleic acid analysis apparatus with isothermal based amplification includes a chamber, a fluid delivery unit, a thermal unit, a rotational driven unit and at least one optical unit. The chamber includes a cartridge mounted therein. The fluid delivery unit is connected with the chamber and adapted to transport reagents within the cartridge for sample purification and/or nucleic acid extraction. The thermal unit is disposed in the chamber and adapted to provide a predefined temperature for nucleic acid amplification. The rotational driven unit is connected with the chamber and capable of rotating the cartridge with a predefined program. The at least one optical unit is disposed on the chamber and includes plural optical components for detection.