Hi Tejas,

JEE is conducted by the Central Board of Secondary Education for admission in various NITs and IITs (if u qualify for advance) across India and MHTCET is conducted by the Maharashtra state board of secondary education for admission in various state government colleges of Maharashtra. JEE's completely based on CBSE 11th and 12th (sci) syllabus and MHTCET on state board 12th (sci) syllabus strictly. In JEE you have an option of writting ur ppr in online (comp based) mode but for MHTCET there's just pen and paper based exam mode.
For JEE: Physics, chemistry and Mathematics carry the equal weightage of marks & number of questions asked i.e. 30 mcqs each carrying four marks and the total is 120 marks each subject. So the grand total is 360. 
For MHTCET: Both Physics and Chemistry include 50 mcqs for 50 marks so this section carries 100 marks. For Mathematics there are 50 mcqs for 100 marks i.e. each carrying 2marks unlike the physics & chemistry section.
So the grand total is 200.
JEE has the negative marking system but MHTCET.
JEE has the duration of 3hrs and MHTCET has 1.5 hr each fr Physics + Chemistry and Mathematics sections (there's a gap in between for the biology paper).
JEE is conducted in 15-20 days after the board exams and MHTCET in 1or 1.5 months. 

Hi,

JEE is entrance exam conducted by CBSE board for admission in NIT. Its Syllabus is based on 11 and 12th. There are total 90 questions. These should be solved within 3 hours. It include more mathematical part. So JEE is hard as compare ro MHCET. Negative marking system is applied for the JEE. MHT CET is a entrance exam conducted by the Maharashtra state board. MHCET is conducted on PCM group of 12 th syllabus. Total 100 questions are therefor 200 marks, from which 100 marks are reserved for the mathematics. There is no any negative marking system. 3 hours are allocated to solve the paper.

Jee mains is the examination conducted for admission in NITs, IITs, IIITs and Government funded technical institutions.MHCET is the exam solely conducted by the state of Maharashtra for admissions into engineering colleges only in the state of maharashtra.