The invention discloses a magnetic nano plugging agent for drilling fluid and a preparation method of the plugging agent. A preparation process comprises the following steps of: adding magnetic nano particles into a dispersion medium and then adding surface modification molecules; uniformly mixing, and heating to react for certain time; and then filtering and drying to obtain the magnetic nano plugging agent. The magnetic nano plugging agent and the preparation method thereof have the advantages that the preparation method of the magnetic nano plugging agent is simple, the process cost is low and industrial production is easy to realize; the grain diameter of the prepared nano plugging agent is small, so that the nano plugging agent can be used for effectively plugging a tiny hole, a micro-crack stratum, and particularly a mud shale stratum; the nano plugging agent has magnetic field responsiveness, and in a drilling process, the nano plugging agent can selectively plug a specific stratum, so that the plugging efficiency is improved. The magnetic nano plugging agent is added into the drilling fluid to obviously improve the comprehensive performance of the drilling fluid; when the magnetic nano plugging agent is used for drilling the tiny hole, the micro-crack stratum and the mud shale stratum, a good effect is obtained.