Based on damage modes of container cranes under earthquake and the characteristic of over-span flexible structures, the anti-seismic design of such machines was investigated. Taking the first crane equipped with isolating device as an example, through dynamic analysis and simulating to anti-seismic crane flexible system under the earthquake and validating analysis and results though the earthquake table tests, efforts was made to research for suitable anti-seismic device and design method for port cranes. The calculation and analysis in the present study could be used as a new way for earthquake resistant design of large-scale flexible portal machine.