Energy efficiency and energy balancing are crucial research issues as per routing protocol designing for self-organized wireless sensor networks (WSNs). Many literatures used the clustering algorithm to achieve energy efficiency and energy balancing, however, there are usually energy holes near the cluster heads (CHs) because of the heavy burden of forwarding. As the clustering problem in lossy WSNs is proved to be a NP-hard problem, many metaheuristic algorithms are utilized to solve the problem. In this paper, a special clustering method called Energy Centers Searching using Particle Swarm Optimization (EC-PSO) is presented to avoid these energy holes and search energy centers for CHs selection. During the first period, the CHs are elected using geometric method. After the energy of the network is heterogeneous, EC-PSO is adopted for clustering. Energy centers are searched using an improved PSO algorithm and nodes close to the energy center are elected as CHs. Additionally, a protection mechanism is also used to prevent low energy nodes from being the forwarder and a mobile data collector is introduced to gather the data. We conduct numerous simulations to illustrate that our presented EC-PSO outperforms than some similar works in terms of network lifetime enhancement and energy utilization ratio.