Active sonar systems are used in the detection and localization of underwater targets. While traditional approaches use pulsed active sonar (PAS) to transmit short bursts, high duty cycle (HDC) sonar systems have been the focus of recent research and can overcome the shortcomings of PAS. Since HDC sonar systems transmit a long pulse train waveform, we must address sub-pulse interference issues, which requires multiple orthogonal sub-pulses and generalized sinusoidal frequency modulated (GSFM) pulses are suitable for this purpose. Unfortunately, conventional GSFM pulse train design methods do not generate an adequate number of orthogonal sub-pulses. Therefore, we propose an improved GSFM pulse train waveform design approach for overcoming the limitations of these conventional methods. The proposed method is organized into two parts, the first focused on the assessment of the auto-correlation, and the second focused on the optimizing the orthogonality between sub-pulses. Cost function is also carefully designed for this purpose. From simulation experiments, we found that the proposed method was able to produce 30 orthogonal sub-pulses and an optimized waveform that demonstrated better detection performance than conventional waveforms under most conditions. We also verified the performance of the proposed method via actual sea experiments, with analysis showing superior performance matching that of simulations. An analysis on the bandwidth parameter $K$ is also conducted and it is found $K = 1.25$ to be the best option.