SQLAlchemy ManyToMany secondary table with additional fields

You will have to switch from using a plain, many-to-many relationship to using an "Association Object", which is basically just taking the association table and giving it a proper class mapping. You'll then define one-to-many relationships to User and Community:

class Membership(db.Model):
    __tablename__ = 'community_members'

    id = db.Column('id', db.Integer, primary_key=True)
    user_id = db.Column(db.Integer, db.ForeignKey('user.id'))
    community_id = db.Column(db.Integer, db.ForeignKey('community.id'))
    time_create = db.Column(db.DateTime, nullable=False, default=func.now())

    community = db.relationship(Community, backref="memberships")
    user = db.relationship(User, backref="memberships")


class Community(db.Model):
    __tablename__ = 'community'

    id = db.Column(db.Integer, primary_key=True)
    name = db.Column(db.String(100), nullable=False, unique=True)

But you may only occasionally be interested in the create time; you want the old relationship back! well, you don't want to set up the relationship twice; because sqlalchemy will think that you somehow want two associations; which must mean something different! You can do this by adding in an association proxy.

from sqlalchemy.ext.associationproxy import association_proxy

Community.members = association_proxy("memberships", "user")
User.communities = association_proxy("memberships", "community")