In resource-constrained project scheduling problem, renewable resource can be expanded into human resource with competency differences, and a flexible resource-constrained project scheduling problem with competency difference is proposed, which is a practical extension close to research and development (R&D) program from the traditional multi-mode resource-constrained project scheduling problem. In order to address the problem, a two-stage algorithm is proposed. In the first stage of precedence constraints satisfactory optimization, a revised ant colony optimization(ACO) algorithm is presented to obtain the feasible activity sequence. In order to accelerate the convergence efficiency and quality, a revised pheromone increment updating operator of ACO with the combination of the serial schedule generation scheme(SSGS) and the resource conflict resolution strategy are used. At the second stage of resource-constraints satisfactory optimization, the obtained optimum precedence activity sequence is taken as the input, and the resource capacity is examined and adjusted one by one until the optimal scheduling solution is obtained. Experimental results show that the optimization model considering the difference of competency is more suitable for the R&D program management practice, and two-stage algorithm can solve the model effectively.