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A cross-layer resource allocation algorithm with fractional frequency reuse and guaranteed diverse QoS is proposed for WiMAX system, where dynamic resource allocation is implemented at both radio network controller (RNC) and base stations (BSs). In order to maximize system frequency reuse ratio to reach the diverse QoS requirements, several novel subchannel allocation schemes are proposed. An RNC coordinates the inter-channel interference (ICI) information of cell edge users (CEUs) based on traffic load at super-frame level, whereas BSs assign channels at frame-level based on real-time traffic load of each cell. Sub-channel borrowing strategy can be adopted between the cell center users (CCUs) and CEUs, if necessary. All the allocation above is hierarchical in order to support multimedia services with different QoS constraints. The performance of the proposed algorithm is evaluated based on the WiMAX dynamical system-level simulation and compared with other existing algorithms.