In its preface, Heavy Gear Second Edition is described as being 100% compatible with its predecessor, however there were a few differences between the two rulebooks.
- The RPG system remained the same.
- The tactical system changed the initiative system, introducing the concept of command points.
The second edition reorganized the material, stripping out some content and replacing it with more setting and background information.
- An eight page color section provided setting maps and material.
- The Vehicle Construction System (VCS) was removed, and reintroduced in the Technical Manual (2nd Edition). Alterations to this system would result in changes to previously published aircraft units (in Field Guide North 2, Field Guide South 2, and primarily Tactical Air Support), but these aircraft were never officially republished.
- The rules for integrating Heavy Gear Fighter were removed.
- The chapter providing army lists for the Northern Guard and Southern MILICIA were removed, officially split and expanded upon in two other products (Northern Guard Army List and Southern MILICIA Army List).
- The mini-module "When All Hell Breaks Lose" was removed.
- A chapter on campaigning was added, including some random scenario generators.
- A 10-page mini-sourcebook covering Peace River was added.
- Character archetypes were modified, with some removed, and some added. Pre-calculated archetype cost listings were added (but rarely included in following products).
Changes between editions of other sourcebooks:
- The Field Guides (Field Guide North 1, Field Guide North 2, Field Guide South 1, Field Guide South 2) were replaced with the Vehicle Compendiums (Northern Vehicles Compendium One: Gears & Striders, Northern Vehicles Compendium Two: Tanks & Artillery, Northern Record Sheets One, Southern Vehicles Compendium One: Gears & Striders, Southern Vehicles Compendium Two: Tanks & Artillery, Southern Record Sheets One).
- Technical Manual (2nd Edition) added 64 pages to Technical Manual (1st Edition). Chapters were rearranged and expanded, new information on hovertanks, aircraft, and spacecraft was added, along with the revamped VCS.
- Life on Terra Nova (2nd edition) reorganized Life on Terra Nova. Material was added to integrate with the A.S.T. Leaguebook and C.N.C.S. Leaguebook sourcebooks, along with another 10-page mini-sourcebook covering Port Arthur.
- Duelist's Handbook (2nd edition) reorganized Duelist's Handbook (1st edition), introducing background, characters, and equipment stats from the Animated Series.