Here we deposit an EEG dataset as well as a MATLAB package for performing Holo-Hilbert spectral analysis (HHSA) on the EEG data. The dataset and code package are primarily for replicating main findings in the paper - *Frontoparietal Beta Amplitude Modulation and its Interareal Cross-frequency Coupling in Visual Working Memory* (**Liang et al., 2021, Neuroscience**). An installation procedure is required if it is the first time a user trying to run “hhsa_tools_d2” in a MATLAB environment. To install the software tool, users should first download hhsa_tools_d2 files to a user-specified folder, followed by changing the MATLAB current directory to this folder and running the installer: “install_hhsa.m”. After completing the above procedures for installation, Scripts for replicating HHSA results in the manuscript can be run. These scripts are in the subfolder: \data_hhsVWM\rep_scripts\. The steps are as follows: 1. Change the matlab directory to D:\data_hhsVWM 2. Run From2LEMD_allSubs.m to perform the two-layer EMD for the data 3. Run tfhh2_allSubs.m to produce the 2D time-AMF HHS of beta oscillation for all the data. 4. Run tconn_allSubs.m to compute the Holo-Hilbert cross-frequency phase clustering (HHCFPC) between theta phase and beta amplitude modulation (AM). 5. Run merge_for_stats.m to merge the data for further statistical analyses. 6. Run tF_clusterperm_corr.m to replicate main findings of beta AM in the manuscript 7. Run tconn_clusterperm_corr.m to replicate main findings of HHCFPC between theta phase and beta AM in the manuscript. Please note that the above installation script will also include a special version of SPM12. Therefore, if there is already a previous version of SPM12 installed in your MATLAB environment, please remove their related paths so that the current hhsa tool can be executed correctly. The package was well tested on MATLAB versions from 2017a to 2018b in WIN64 platform.