Time-domain analyses of seismic waveforms have revealed diverse source complexity in large earthquakes (Mw>7). However, source characteristics of small earthquakes have been studied by assuming a simple rupture pattern in the frequency domain. This study utilized high-quality seismic network data from Japan to systematically address the source complexities and radiated energies of Mw 3–7 earthquakes in the time domain. We first determined the apparent moment-rate functions (AMRFs) of the earthquakes using the empirical Green’s functions. Some of the AMRFs showed multiple peaks, suggesting complex ruptures at multiple patches. We then estimated the radiated energies (𝐸𝑅) of 1736 events having more than ten reliable AMRFs. The scaled energy (𝑒𝑅=𝐸𝑅/𝑀0) did not strongly depend on the seismic moment (𝑀0), focal mechanisms, or depth. The median value of 𝑒𝑅 was 3.7×10-5, which is comparable to those of previous studies; however, 𝑒𝑅 varied by approximately one order of magnitude among earthquakes. Additionally, we measured the source complexity based on the radiated energy enhancement factor (𝑅𝐸𝐸𝐹). The values of 𝑅𝐸𝐸𝐹 differed among earthquakes, implying diverse source complexity. The values of 𝑅𝐸𝐸𝐹 did not show strong scale dependence for Mw 3–7 earthquakes, suggesting that the source diversity of smaller earthquakes is similar to that of larger earthquakes at their representative spatial scales. Applying a simple spectral model (e.g., the ω2-source model) to complex ruptures may produce substantial estimation errors of source parameters.