It means that whatever bad deeds Dr. Jekyll had committed, compared to Mr. Hyde's, is nothing. In other words, Mr. Hyde's actions are far more evil than Dr. Jekyll's.

This Mr. Hyde must have secrets of his own ー black secrets, by the look of him － secrets compared to which poor jekill's worst would be like sunshine. Mr. Hyde has negative (black) secrets. = Perhaps he has done terrible things, or thinks awful thoughts. In comparison, Jekill's secrets, even his worse ones, are not so bad at all. = Jekill probably hasn't done anything very bad.

my hyde is hiding very dark secrets, in which jekyll's darkest secrets would pale in comparison to his