For designing a digital High Frequency (HF) radio communication system in the skywave propagation mode, Delay spread and Doppler spread are the fundamental parameters of ionosphere channel characteristics that need to be known. Although the International Telecommunication Union (ITU) already provides general classification values for three different regions and conditions as a recommendation, the empirical Delay spread and Doppler spread values are still needed for an optimum design. As the role of HF communication in Indonesia is still important and its development technology is continued, the empirical data of ionosphere channel characteristics are also needed. However, the comprehensive empirical data of ionosphere channel characteristics over Indonesia is difficult to find. In this research, we developed an Ionosphere Channel Impulse Response (CIR) measurement system based on Software Defined Radio (SDR) with purpose to obtain the empirical values of Delay spread and Doppler spread. The measurement system is placed in Java Island Indonesia, which is in the Low latitude - Equatorial Ionosphere Anomaly (EIA) region. The specification of the system was determined based on the increased values of ITU parameters for low-latitude regions in order to be able to capture the possibility of higher values. The early measurement result shows slightly different values from ITU recommendation which is probably due to the EIA regions effect. This system is ready to collect further data to characterize the ionospheric communication channel comprehensively and investigate the space weather impact on HF communication systems.