The invention discloses an in-situ remediation method of a heavy metal polluted site, which is characterized in that a stabilizing agent is completely covered on the polluted site through throwing a heavy metal-chelating stabilizing agent on the polluted site with low water content, thus secondary pollution of heavy metal pollutants to the environment is avoided; the polluted site is turned and stirred for multiple times by using an amphibious excavator, the stabilizing agent and the heavy metal pollutants can fully react to form a stable material, thus ensuring that the leaching concentration of heavy metals is in an allowable range; and concretion is carrying out for multiple days through airing, the treated site can be used for soil improvement, landscaping or landfill backfilling according to difference of the water contents and the heavy metal in and outlet concentrations. Therefore, compared with the prior art, the in-situ remediation method has the advantages of ensuring stabilizing effect of the heavy metals, importantly solving the problem of soft foundation encountered by common stirring modes, and ensuring that chemicals are fully mixed with the polluted soil through adopting common excavators for site stirring if the foundation is allowable.