This paper presents a new method for improving transition fault coverage in hybrid scan testing. It is based on a novel test application scheme, in order to break the functional dependence of broadside testing. The new technique analyzes the automatic test pattern generation conflicts in broadside test generation and skewed-load test generation, and tries to control the flip-flops with the most influence on fault coverage. The conflict-driven selection method selects some flip-flops that work in the enhanced scan mode or skewed-load scan mode. And the conflict-driven reordering method distributes the selected flip-flops into different chains. In the multiple scan chain architecture, to avoid too many scan-in pins, some chains are driven by the same scan-in pin to construct a tree-based architecture. Based on the architecture, the new test application scheme allows some flip-flops to work in enhanced scan or skewed-load mode, while most of others to work in the traditional broadside scan mode. With the efficient conflict-driven selection and reordering schemes, fault coverage is improved greatly, which can also reduce test application time and test data volume. Experimental results show that fault coverage based on the proposed method is comparable that of enhanced scan.