In this manuscript, we study properties of long-term optical variability of a large sample of 106 SDSS spectroscopically confirmed AGN with double-peaked broad low-ionization emission lines (double-peaked emitters). The long-term optical light curves over 8 years are collected from the Catalina Sky Surveys Data Release 2. And, the Damped Random Walk (DRW) process is applied to describe the long-term variability of the double-peaked emitters. Meanwhile, the same DRW process is applied to long-term optical light curves of more than 7000 spectroscopically confirmed normal quasars in the SDSS Stripe82 Database. Then, we can find that the DRW process determined rest-frame intrinsic variability timescales $\ln(\tau/{\rm days})$ are about 5.8 and about 4.8 for the double-peaked emitters and for the normal quasars, respectively. The statistically longer intrinsic variability timescales can be confirmed in the double-peaked emitters, after considerations of necessary effects, such as the effects from different distributions of redshift, BH mass and accretion rate between the double-peaked emitters and the normal quasars. Moreover, a radial dependence of accretion rate $\dot{m}_{\rm R}~\propto~R^\beta$ with larger values of $\beta$ could be an acceptable interpretation of the longer intrinsic variability timescales in the double-peaked emitters. Therefore, there are different intrinsic properties of emission regions between the double-peaked emitters and the normal quasars. The double-peaked emitters can be well treated as an unique subclass of AGN.