The invention discloses a manufacturing method of an MEMS chip insensitive to packaging stress. The manufacturing method comprises the steps of firstly, taking an SOI wafer, forming a lower electrode by use of top-layer Si and etching the top-layer Si to form lower electrode patterns, secondly, taking a single crystal Si wafer and performing photoetching and Si etching to form a substrate wafer, thirdly, aligning the SOI wafer to the substrate wafer, performing silicon-silicon dioxide bonding and annealing to form a bonded wafer, and grinding the bottom-layer Si of the SOI wafer in the bonded wafer to form an MEMS activity structure layer, fourthly, depositing a metal layer on the MEMS activity structure layer to form a metal pad, fifthly, etching the MEMS activity structure layer and releasing the MEMS activity structure layer, sixthly, taking a single-crystal Si wafer, and performing photoetching and Si etching to form a cover plate wafer, seventhly, aligning and bonding the cover plate wafer to the bonded wafer and annealing to form a sealed wafer, and finally cutting the cover plate wafer and the sealed wafer to obtain the MEMS chip. The manufacturing method is short in process and high in rate of finished products; the manufactured MEMS chip is insensitive to the packaging stress.