In the Long Term Evolution Advanced (LTE-A) heterogeneous networks (Het-Nets), smallcell is an emerging and key item, providing improved service coverage and high spectral efficiency with low power. However, the number and location arrangement of smallcell is always changing in reality, the interference scenario is also different. In order to reduce the layer-to-layer interference in uncertain deployment of smallcell, a method of frequency domain self-organizing interference coordination technology is proposed in this paper. In this method, the total spectrum bandwidth is divided into two parts according to a frequency partition ratio. One part of the bandwidth is called protected band where macrocell's transmission power will be reduced in an adaptively controlled way to schedule the edge UEs of smallcell and the center UEs of macrocell, another is named unprotected band to schedule the macro edge UEs and smallcells' center UEs. Thus, the edge UEs of smallcell could be protected under the condition of not losing too much macrocells' performance. The system-level simulation results show that the proposed scheme can achieve superior system performance improvements, and higher cell-edge user data rate.