Black silicon electrodes with inverted pyramid arrays (SiIPs) are promising for efficient photoelectrochemical water splitting due to their excellent photoelectric properties and quasi-hydrophilicity. In this work, an elaborate study on microstructure regulation of SiIP photocathodes is reported. We find that on SiIPs where sidewalls have been processed with copper-assisted chemical etching (Cu-ACE), there are vast numbers of micro-pits distributed (deep holes and shallow grooves) that exactly determine electrode performance, which is a result of homogeneous Cu2+ oxidation of Si. Furthermore, SiIP microstructural features can be effectively adjusted via controlling the etchant composition and introducing alkali post-treatment. Taking the trade-off between light trapping ability and charge separation capacity into consideration, we optimized the hydrogen evolution reaction (HER) activity of a SiIP photocathode, and its onset potential was decreased to -0.35 V vs. RHE. On this basis, we constructed reliable heterojunctions to further improve the sluggish HER kinetics. The optimized SiIPs/TiO2/MoSx cathode exhibits a considerable photocurrent density of 9.45 mA cm-2 at zero HER overpotential for 18 h in acidic media. Notably, our work presents a detailed physical insight into micro-pit formation and elimination in Cu-ACE, and describes the dependency of SiIP-based electrode performance on the microstructure morphology, paving a new way for its potential application in unbiased overall water splitting.