A numerical control system for laser cutting an SMT stencil includes a mechanical control portion (2) and a laser control portion (3). The mechanical control portion includes a first main control system (21), a first host computer isolation interface (22), a first communication interface controller (24), a first optoelectronic/magnetic isolator (25), and a first isolated input/output interface (23) coupled to a mechanical transmission device. Similarly, the laser control portion includes a second main control system (31), a second host computer isolation interface (32), a second communication interface controller (34), a second optoelectronic/magnetic isolator (35), and a second isolated input/output interface (33) coupled to a laser cutting device. The first and second main control systems are connected with the host computer via the respective first and second host computer isolation interfaces. The first and second optoelectronic/magnetic isolators are connected with a slave computer. The numerical control system can be further divided into a cutting management module (4) and a stencil output module (5). A numerical control method associated with the above numerical control system for laser cutting an SMT stencil is also disclosed.