The hybrid mobile ad hoc network (H-MANET) consist of self organized mobile nodes connected over radio frequency (RF) and free space optics (FSO) based wireless links. Due to limited transmission range of RF based network, the communication between two RF based MANETs are carried out by using FSO link. We have design two different clusters of RF based MANETs. Both clusters are connected by two FSO nodes, which are also a part of an individual RF based network. In our research work, we have analyze the performance of H-MANET in terms of throughput for different network areas (1000m× 1000m, 2000m × 2000m and 3000m× 3000m) and scaling number of nodes up to 200. We have used the same protocol combinations (AODV-AODV, AOMDV-AOMDV, DSDV-DSDV and OLSR-OLSR) for two different RF based networks and joint together by FSO link for analyzing the effectiveness of H-MANET. The simulation experiment is carried out by using network simulator tool (NS 2.35) and data analysis with graphical representation has been done by using MATLAB (R) .