Space microscientific instruments require power supplies that are sustainable, stable, and long life. A micro-radioisotope thermoelectric generator can be used as a sustainable long-life power supply for low-power-device applications. This study innovatively proposes micro stacked-integrated annular-radial radioisotope thermoelectric generator and prepares a multilayer prototype to drive various LEDs as a demo. A high-performance micro-radioisotope thermoelectric generator module based on a flexible printed circuit is designed and prepared by screen printing. At a temperature difference of 48 K, the voltage density is 2.21 V cm−3, and the power density is 514.25 μW cm−3. When loaded with 1.564 W heat sources, a 10-layer prototype generates an open-circuit voltage of 0.815 V, a short-circuit current of 0.551 mA, and an output power of 114.38 μW. The maximum series voltages are 0.929 and 2.2 V for the 10- and 30-layer prototypes. The short-circuit current of the 5-layer parallel prototype is 1.18 mA, and the voltage is hardly reduced. In the impact evaluation on ambient temperature, the electrical output of the prototype increases with increased temperature (−30 °C–120 °C). In the different configurations of the prototype, the 10-layer, 30-layer series, and 5-layer parallel prototypes are proposed, thereby providing considerable output. The developed generator is expected to provide reliable power support for space microscientific instruments.