Developing acid-tolerant magnetothermal nanoplatform with robust drug loading capacity for remote controlled drug release is challenging in the harsh acid environment of stomach. Herein, a nanopomegranate-type magnetothermal controllable drug release platform (FeCo@G@MSN), consisted of magnetothermal convertor (graphene-isolated FeCo nanocrystal core, FeCo@G) and drug reservoir (mesoporous silica, MSN), with acid-tolerant hierarchical structure was developed. Benefiting from the acid tolerance of graphene and MSN, FeCo@G@MSN was stable in 1 M hydrochloric acid for more than 12 h. The nanopomegranate-type hierarchical structure endowed FeCo@G@MSN with high saturation magnetization (114.9 emu/g) to generate a magnetothermal effect and large specific surface area (293.7 m/g) to provide ample space for drug loading. As a proof of concept, a heat-triggered nitric oxide (NO) precursor was loaded, and NO were controlled released by breaking of S-NO bonds through localized heat derived from magnetothermal effect of FeCo@G, resulting in an inhibition effect towards Helicobacter pylori. A chemotherapeutic drug (doxorubicin, DOX) was also loaded and controlled released by breaking of hydrogen bonds between silica and DOX under remote an alternating magnetic field, thus exhibiting an inhibition effect towards gastric cancer cells. This work provides an efficient strategy to exploit magnetothermal controlled drug release platform and offers inspiration for the treatment of gastric diseases.