With the continuously increasing capacity of modern power system, the problem of excessive short circuit current is becoming more and more severe. Not only three-phase short circuit current (TSCC), but also single-phase short circuit current (SSCC) has exceeded the upper limit. In this paper, a two-step optimization method to limit both of TSCC and SSCC is proposed. Different characteristics of various limiting measures have been analyzed. The limiting measures for TSCC can limit SSCC. However, the limiting measures for SSCC have no effect on TSCC. The configuration for TSCC limiting measures is optimized using adaptive hybrid PSO algorithm firstly, which considers the cost and grid tightness at the same time. After this step, the excessive TSCC should be eliminated. Based on the obtained optimal configuration for TSCC, the optimization for SSCC continues, which makes a two-step short circuit current limiting method. The optimal configuration for SSCC limiting measures is obtained using hybrid integer programming with minimum cost as the objective. Given the limiting effect of TSCC limiting measures for SSCC and high calculating speed of hybrid integer programming, the optimization for SSCC might be omitted in many actual cases, which makes a faster optimization speed therefore is more suitable for online application. The effectiveness of the proposed two-step optimization method is validated by the cases of two actual regional power systems.