As the feature size keeps scaling down and the circuit complexity increases rapidly, a more advanced hybrid lithography, which combines multiple patterning and e-beam lithography (EBL), is promising to further enhance the pattern resolution. In this paper, we formulate the layout decomposition problem for this hybrid lithography as a minimum vertex deletion K-partition problem, where K is the number of masks in multiple patterning. Stitch minimization and EBL throughput are considered uniformly by adding a virtual vertex between two feature vertices for each stitch candidate during the conflict graph construction phase. For K = 2, we propose a primal-dual method for solving the underlying minimum odd-cycle cover problem efficiently. In addition, a chain decomposition algorithm is employed for removing all 'non-cyclable' edges. For K > 2, we propose a random-initialized local search method that iteratively applies the primal-dual solver. Experimental results show that compared with a two-stage method, our proposed methods reduce the EBL usage by 64.4% with double patterning and 38.7% with triple patterning on average for the benchmarks.